A Computational Study of Lithium Carbamate Synthetic Intermediate Structures and Aggregation

Computational quantum chemistry was used to investigate the structures of lithium carbamates in the gas phase and in ethereal solvents. These compounds act as nucleophiles with either inversion or retention of configuration at the chiral center and knowledge of the aggregation state is the first step in understanding the reactivity. The sterically hindered lithium phenyl carbamate is calculated to exist largely as the ether or THF solvated monomer in solution. Higher aggregates are possible in the gas phase, which is often taken as an approximation for solutions in non-polar solvents

Influence of ocean circulation changes on the inter-annual variability of American eel larval dispersal

Author Posting. © Association for the Sciences of Limnology and Oceanography, 2016. This article is posted here by permission of Association for the Sciences of Limnology and Oceanography for personal use, not for redistribution. The definitive version was published in Limnology and Oceanography 61 (2016): 1574–1588, doi:10.1002/lno.10297.American eel (Anguilla rostrata) complete their life cycle by migrating from the east coast of North America to Sargasso Sea, where they spawn planktonic eggs and dye. Larvae that develop from eggs need to return to North American coastal waters within the first year of life and are influenced by the oceanic currents during this journey. A coupled physical–biological model is used to investigate the extent to which inter-annual changes in the ocean circulation affect the success rates of larvae in reaching coastal nursery habitats. Our results suggest that natural oceanic variability can lead to changes in larval success rates by a factor of 2. Interannual variation in success rates are strongly affected by the Gulf Stream inertial overshoot events, with the largest success in years with an inertial overshoot and the smallest in years with a straighter and more southern configuration of the Gulf Stream downstream of Cape Hatteras. The mean Gulf Stream length and latitude between 75W and 70W longitude can be used as proxies for characterizing the overshoot events and can be converted into success rates using linear regression.I.I.R. and L.J.P. were supported by grant 85464100 (OCE-1154641) from the National Science Foundation. M.S.L. gratefully acknowledges support from the National Science Foundation

Flow and hydraulics near the sill of Hood Canal, a strongly sheared, continuously stratified fjord

Author Posting. © American Meteorological Society, 2010. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Journal of Physical Oceanography 40 (2010): 1087-1105, doi:10.1175/2010JPO4312.1.Hood Canal, a long fjord in Washington State, has strong tides but limited deep-water renewal landward of a complex constriction. Tide-resolving hydrographic and velocity observations at the constriction, with a depth-cycling towed body, varied markedly during three consecutive years, partly because of stratification variations. To determine whether hydraulic control is generally important and to interpret observations of lee waves, blocking, and other features, hydraulic criticality is estimated over full tidal cycles for channel wide internal wave modes 1, 2, and 3, at five cross-channel sections, using mode speeds from the extended Taylor–Goldstein equation. These modes were strongly supercritical during most of ebb and flood on the gentle seaward sill face and for part of flood at the base of the steep landward side. Examining local criticality along the thalweg found repeated changes between mode 1 being critical and supercritical approaching the sill crest during flood, unsurprising given local minima and maxima in the cross-sectional area, with the sill crest near a maximum. Density crossing the sill sometimes resembled an overflow with an internal hydraulic control at the sill, followed by a hydraulic jump or lee wave. Long-wave speeds, however, suggest cross waves, particularly along the shallower gentler side, where flow downstream of a large-amplitude wave was uniformly supercritical. Supercritical approaching the sill, peak ebb was critical to mode 1 and supercritical to modes 2 and 3 at the base while forming a sluggish dome of dense water over the sill. Full interpretation exceeds observations and existing theory.Washington State Sea Grant funded collection of these observations and the Office of Naval Research their publication. Pratt’s efforts were supported by the National Science Foundation under Grant OCE-0525729

Formation and spreading of Red Sea Outflow Water in the Red Sea

Author Posting. © American Geophysical Union, 2015. This article is posted here by permission of American Geophysical Union for personal use, not for redistribution. The definitive version was published in Journal of Geophysical Research: Oceans 120 (2015): 6542–6563, doi:10.1002/2015JC010751.Hydrographic data, chlorofluorocarbon-12 (CFC-12) and sulfur hexafluoride (SF6) measurements collected in March 2010 and September–October 2011 in the Red Sea, as well as an idealized numerical experiment are used to study the formation and spreading of Red Sea Outflow Water (RSOW) in the Red Sea. Analysis of inert tracers, potential vorticity distributions, and model results confirm that RSOW is formed through mixed-layer deepening caused by sea surface buoyancy loss in winter in the northern Red Sea and reveal more details on RSOW spreading rates, pathways, and vertical structure. The southward spreading of RSOW after its formation is identified as a layer with minimum potential vorticity and maximum CFC-12 and SF6. Ventilation ages of seawater within the RSOW layer, calculated from the partial pressure of SF6 (pSF6), range from 2 years in the northern Red Sea to 15 years at 17°N. The distribution of the tracer ages is in agreement with the model circulation field which shows a rapid transport of RSOW from its formation region to the southern Red Sea where there are longer circulation pathways and hence longer residence time due to basin wide eddies. The mean residence time of RSOW within the Red Sea estimated from the pSF6 age is 4.7 years. This time scale is very close to the mean transit time (4.8 years) for particles from the RSOW formation region to reach the exit at the Strait of Bab el Mandeb in the numerical experiment.King Abdullah University of Science and Technology (KAUST) Grant Numbers: USA 00002, KSA 00011, KSA 00011/02; National Science Foundation; WHOI Academic Program Office Grant Number: OCE09270172016-03-2

Quasi-chemical Theories of Associated Liquids

It is shown how traditional development of theories of fluids based upon the concept of physical clustering can be adapted to an alternative local clustering definition. The alternative definition can preserve a detailed valence description of the interactions between a solution species and its near-neighbors, i.e., cooperativity and saturation of coordination for strong association. These clusters remain finite even for condensed phases. The simplest theory to which these developments lead is analogous to quasi-chemical theories of cooperative phenomena. The present quasi-chemical theories require additional consideration of packing issues because they don't impose lattice discretizations on the continuous problem. These quasi-chemical theories do not require pair decomposable interaction potential energy models. Since calculations may be required only for moderately sized clusters, we suggest that these quasi-chemical theories could be implemented with computational tools of current electronic structure theory. This can avoid an intermediate step of approximate force field generation.Comment: 20 pages, no figures replacement: minor typographical corrections, four references added, in press Molec. Physics 199

Exploring interannual variability in potential spawning habitat for Atlantic bluefin tuna in the Slope Sea

© The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Rypina, I. I., Dotzel, M. M., Pratt, L. J., Hernandez, C. M., & Llopiz, J. K. Exploring interannual variability in potential spawning habitat for Atlantic bluefin tuna in the Slope Sea. Progress in Oceanography, 192, (2021): 102514, https://doi.org/10.1016/j.pocean.2021.102514.The Slope Sea in the Northwest Atlantic Ocean, located between the Gulf Stream and the continental shelf of the Northeast United States, is a recently-documented possible major spawning ground for Atlantic bluefin tuna (Thunnus thynnus). Larval surveys and a habitat modeling study have shown that suitable spawning habitat occurs in the Slope Sea, but the degree to which this habitat varies interannually is an open question. Here, we perform a decade-long (2009–2018) numerical modeling analysis, with simulated larvae released uniformly throughout the Slope Sea, to investigate the interannual variability in the water temperature and circulation criteria deemed necessary for successful spawning. We also quantify the influence of Gulf Stream meanders and overshoot events on larval retention and their effect on habitat suitability rates throughout the Slope Sea, defined as the percentage of simulated larvae released at a given location that satisfy criteria related to water temperature and retention near nursery habitat. Average environmental oceanographic conditions over the decade are most favorable in the western part of the Slope Sea, specifically in the Slope Gyre and away from the immediate vicinity of the Gulf Stream. Variability in domain- and summertime-averaged yearly spawning habitat suitability rates is up to 25% of the mean decadal-averaged values. Yearly habitat suitability correlates strongly with the Gulf Stream overshoot but does not correlate well with other oceanographic variables or indices, so an overshoot index can be used as a sole oceanographic proxy for predicting yearly bluefin spawning habitat suitability in the Slope Sea. Selective spawning can weaken the correlation between habitat suitability and Gulf Stream overshoot. Effort should be put towards collecting observational data against which we could validate our findings.This work was funded by a US National Science Foundation (NSF) grant (OCE-1558806) awarded to IIR, LJP, and JKL. MMD was supported by an NSF Graduate Research Fellowship. CMH was partially supported by the Adelaide and Charles Link Foundation and the J. Seward Johnson Endowment in support of the Woods Hole Oceanographic Institution’s Marine Policy Center

Chaotic advection in a steady, three-dimensional, Ekman-driven eddy

Author Posting. © Cambridge University Press, 2013. This article is posted here by permission of Cambridge University Press for personal use, not for redistribution. The definitive version was published in Journal of Fluid Mechanics 738 (2014): 143-183, doi:10.1017/jfm.2013.583.We investigate and quantify stirring due to chaotic advection within a steady, three-dimensional, Ekman-driven, rotating cylinder flow. The flow field has vertical overturning and horizontal swirling motion, and is an idealization of motion observed in some ocean eddies. The flow is characterized by strong background rotation, and we explore variations in Ekman and Rossby numbers, E and Ro, over ranges appropriate for the ocean mesoscale and submesoscale. A high-resolution spectral element model is used in conjunction with linear analytical theory, weakly nonlinear resonance analysis and a kinematic model in order to map out the barriers, manifolds, resonance layers and other objects that provide a template for chaotic stirring. As expected, chaos arises when a radially symmetric background state is perturbed by a symmetry-breaking disturbance. In the background state, each trajectory lives on a torus and some of the latter survive the perturbation and act as barriers to chaotic transport, a result consistent with an extension of the KAM theorem for three-dimensional, volume-preserving flow. For shallow eddies, where E is O(1), the flow is dominated by thin resonant layers sandwiched between KAM-type barriers, and the stirring rate is weak. On the other hand, eddies with moderately small E experience thicker resonant layers, wider-spread chaos and much more rapid stirring. This trend reverses for sufficiently small E, corresponding to deep eddies, where the vertical rigidity imposed by strong rotation limits the stirring. The bulk stirring rate, estimated from a passive tracer release, confirms the non-monotonic variation in stirring rate with E. This result is shown to be consistent with linear Ekman layer theory in conjunction with a resonant width calculation and the Taylor–Proudman theorem. The theory is able to roughly predict the value of E at which stirring is maximum. For large disturbances, the stirring rate becomes monotonic over the range of Ekman numbers explored. We also explore variation in the eddy aspect ratio.L.J.P., I.I.R., T.M.O. and P.W. have been supported on DOD (MURI) grant N000141110087, administered by the Office of Naval Research. I.I.R. and L.J.P. received additional support from Grant NSF-OCE-0725796 from the National Science Foundation.2014-12-0

Mixed Aggregates of 1-Methoxyallenyllithium with Lithium Chloride

A combined computational and 13C NMR study was used to investigate the formation of mixed aggregates of 1-methoxyallenyllithium and lithium chloride in tetrahydrofuran (THF) solution. The observed and calculated chemical shifts, as well as the calculated free energies of mixed aggregate formation (MP2/6-31+G(d)), are consistent with the formation of a mixed dimer as the major species in solution. Free energies of mixed dimer, trimer, and tetramer formation were calculated by using the B3LYP and MP2 methods and the 6-31+G(d) basis set. The two methods generated different predictions of which mixed aggregates will be formed, with B3LYP/6-31+G(d) favoring mixed trimers and tetramers in THF solution, and MP2/6-31+G(d) favoring mixed dimers. Formation of the sterically unhindered mixed dimers is also consistent with the enhanced reactivity of these compounds in the presence of lithium chloride. The spectra are also consistent with some residual 1-methoxyallenyllithium tetramer, as well as small amounts of higher mixed aggregates. Although neither computational method is perfect, for this particular system, the calculated free energies derived using the MP2 method are in better agreement with experimental data than those derived using the B3LYP method

Self Consistent Molecular Field Theory for Packing in Classical Liquids

Building on a quasi-chemical formulation of solution theory, this paper proposes a self consistent molecular field theory for packing problems in classical liquids, and tests the theoretical predictions for the excess chemical potential of the hard sphere fluid. Results are given for the self consistent molecular fields obtained, and for the probabilities of occupancy of a molecular observation volume. For this system, the excess chemical potential predicted is as accurate as the most accurate prior theories, particularly the scaled particle (Percus-Yevick compressibility) theory. It is argued that the present approach is particularly simple, and should provide a basis for a molecular-scale description of more complex solutions.Comment: 6 pages and 5 figure

Assimilating Lagrangian data for parameter estimation in a multiple-inlet system

© The Author(s), 2017. This is the author's version of the work. It is posted here under a nonexclusive, irrevocable, paid-up, worldwide license granted to WHOI. It is made available for personal use, not for redistribution. The definitive version was published in Ocean Modelling 113 (2017): 131-144, doi:10.1016/j.ocemod.2017.04.001.Numerical models of ocean circulation often depend on parameters that must be tuned to match either results from laboratory experiments or field observations. This study demonstrates that an initial, suboptimal estimate of a parameter in a model of a small bay can be improved by assimilating observations of trajectories of passive drifters. The parameter of interest is the Manning's n coefficient of friction in a small inlet of the bay, which had been tuned to match velocity observations from 2011. In 2013, the geometry of the inlet had changed, and the friction parameter was no longer optimal. Results from synthetic experiments demonstrate that assimilation of drifter trajectories improves the estimate of n, both when the drifters are located in the same region as the parameter of interest and when the drifters are located in a different region of the bay. Real drifter trajectories from field experiments in 2013 also are assimilated, and results are compared with velocity observations. When the real drifters are located away from the region of interest, the results depend on the time interval (with respect to the full available trajectories) over which assimilation is performed. When the drifters are in the same region as the parameter of interest, the value of n estimated with assimilation yields improved estimates of velocity throughout the bay.This work was supported by: Department of Defense Multidisciplinary University Research Initiative (MURI) [grant N000141110087], administered by the Office of Naval Research; the National Science Foundation (NSF); the National Oceanic and Atmospheric Administration (NOAA); NOAA's Climate Program Office; the Department of Energy's Office for Science (BER); and the Assistant Secretary of Defense (Research & Development)