Calculating energy derivatives for quantum chemistry on a quantum computer

Modeling chemical reactions and complicated molecular systems has been proposed as the `killer application' of a future quantum computer. Accurate calculations of derivatives of molecular eigenenergies are essential towards this end, allowing for geometry optimization, transition state searches, predictions of the response to an applied electric or magnetic field, and molecular dynamics simulations. In this work, we survey methods to calculate energy derivatives, and present two new methods: one based on quantum phase estimation, the other on a low-order response approximation. We calculate asymptotic error bounds and approximate computational scalings for the methods presented. Implementing these methods, we perform the world's first geometry optimization on an experimental quantum processor, estimating the equilibrium bond length of the dihydrogen molecule to within 0.014 Angstrom of the full configuration interaction value. Within the same experiment, we estimate the polarizability of the H2 molecule, finding agreement at the equilibrium bond length to within 0.06 a.u. (2% relative error).Comment: 19 pages, 1 page supplemental, 7 figures. v2 - tidied up and added example to appendice

Report on the “Trait-based approaches to ocean life” scoping workshop, October 5-8, 2015

"Trait-based Approaches to Ocean Life” Scoping Workshop, October 5-8, 2015, Waterville Valley, NH, USAFrom the introduction: Marine ecosystems are rich and biodiverse, often populated by thousands of competing and interacting species with a vast range of behaviors, forms, and life histories. This great ecological complexity presents a formidable challenge to understanding how marine ecosystems are structured and controlled, but also how they respond to natural and anthropogenic changes. The trait-based approach to ocean life is emerging as a novel framework for understanding the complexity, structure, and dynamics of marine ecosystems, but also their broader significance. Rather than considering species individually, organisms are characterized by essential traits that capture key aspects of diversity. Trait distributions in the ocean emerge through evolution and natural selection, and are mediated by the environment, biological interactions, anthropogenic drivers, and organism behavior. Because trait variations within and across communities lead to variation in the rates of crucial ecosystem functions such as carbon export, this mechanistic approach sheds light on how variability in the environment, including climate change, impacts marine ecosystems, biogeochemical cycles, and associated feedbacks to climate and society.Funding from the National Science Foundation and National Aeronautics and Space Administration), the Simons Foundation, and the Gordon and Betty Moore Foundation

Capturing optically important constituents and properties in a marine biogeochemical and ecosystem model

We present a numerical model of the ocean that couples a three-stream radiative transfer component with a marine biogeochemical–ecosystem component in a dynamic three-dimensional physical framework. The radiative transfer component resolves the penetration of spectral irradiance as it is absorbed and scattered within the water column. We explicitly include the effect of several optically important water constituents (different phytoplankton functional types; detrital particles; and coloured dissolved organic matter, CDOM). The model is evaluated against in situ-observed and satellite-derived products. In particular we compare to concurrently measured biogeochemical, ecosystem, and optical data along a meridional transect of the Atlantic Ocean. The simulation captures the patterns and magnitudes of these data, and estimates surface upwelling irradiance analogous to that observed by ocean colour satellite instruments. We find that incorporating the different optically important constituents explicitly and including spectral irradiance was crucial to capture the variability in the depth of the subsurface chlorophyll a (Chl a) maximum. We conduct a series of sensitivity experiments to demonstrate, globally, the relative importance of each of the water constituents, as well as the crucial feedbacks between the light field, the relative fitness of phytoplankton types, and the biogeochemistry of the ocean. CDOM has proportionally more importance at attenuating light at short wavelengths and in more productive waters, phytoplankton absorption is relatively more important at the subsurface Chl a maximum, and water molecules have the greatest contribution when concentrations of other constituents are low, such as in the oligotrophic gyres. Scattering had less effect on attenuation, but since it is important for the amount and type of upwelling irradiance, it is crucial for setting sea surface reflectance. Strikingly, sensitivity experiments in which absorption by any of the optical constituents was increased led to a decrease in the size of the oligotrophic regions of the subtropical gyres: lateral nutrient supplies were enhanced as a result of decreasing high-latitude productivity. This new model that captures bio-optical feedbacks will be important for improving our understanding of the role of light and optical constituents on ocean biogeochemistry, especially in a changing environment. Further, resolving surface upwelling irradiance will make it easier to connect to satellite-derived products in the future

Iron conservation by reduction of metalloenzyme inventories in the marine diazotroph Crocosphaera watsonii

The marine nitrogen fixing microorganisms (diazotrophs) are a major source of nitrogen to open ocean ecosystems and are predicted to be limited by iron in most marine environments. Here we use global and targeted proteomic analyses on a key unicellular marine diazotroph Crocosphaera watsonii to reveal large scale diel changes in its proteome, including substantial variations in concentrations of iron metalloproteins involved in nitrogen fixation and photosynthesis, as well as nocturnal flavodoxin production. The daily synthesis and degradation of enzymes in coordination with their utilization results in a lowered cellular metalloenzyme inventory that requires ~40% less iron than if these enzymes were maintained throughout the diel cycle. This strategy is energetically expensive, but appears to serve as an important adaptation for confronting the iron scarcity of the open oceans. A global numerical model of ocean circulation, biogeochemistry and ecosystems suggests that Crocosphaera’s ability to reduce its iron-metalloenzyme inventory provides two advantages: It allows Crocosphaera to inhabit regions lower in iron and allows the same iron supply to support higher Crocosphaera biomass and nitrogen fixation than if they did not have this reduced iron requirement.National Science Foundation (U.S.). Chemical and Biological Oceanography Program (OCE-0452883)National Science Foundation (U.S.). Chemical and Biological Oceanography Program (OCE-0752291)National Science Foundation (U.S.). Chemical and Biological Oceanography Program (OCE-0723667)National Science Foundation (U.S.). Chemical and Biological Oceanography Program (OCE-0928414)National Science Foundation (U.S.). Polar Program (ANT-0732665)United States. Environmental Protection Agency (Star Fellowship)Woods Hole Oceanographic Institution. Ocean Life InstituteCenter for Microbial Oceanography: Research and EducationCenter for Environmental Bioinorganic Chemistr

MIT Integrated Global System Model (IGSM) Version 2: Model Description and Baseline Evaluation

Abstract in HTML and technical report in PDF available on the Massachusetts Institute of Technology Joint Program on the Science and Policy of Global Change website (http://mit.edu/globalchange/www/).The MIT Integrated Global System Model (IGSM) is designed for analyzing the global environmental changes that may result from anthropogenic causes, quantifying the uncertainties associated with the projected changes, and assessing the costs and environmental effectiveness of proposed policies to mitigate climate risk. This report documents Version 2 of the IGSM, which like the previous version, includes an economic model for analysis of greenhouse gas and aerosol precursor emissions and mitigation proposals, a coupled atmosphere-ocean-land surface model with interactive chemistry, and models of natural ecosystems. In this global framework the outputs of the combined anthropogenic and natural emissions models provide the driving forces for the coupled atmospheric chemistry and climate models. Climate model outputs then drive a terrestrial model predicting water and energy budgets, CO2, CH4, and N2O fluxes, and soil composition, which feed back to the coupled climate/chemistry model. The first version of the integrated framework (which we will term IGSM1) is described in Prinn et al. (1999) and in publications and Joint Program Reports and Technical Notes provided on the Program’s website (http://mit.edu/globalchange/). Subsequently, upgrades of component model capabilities have been achieved, allowing more comprehensive and realistic studies of global change. Highlights of these improvements include: a substantially improved economics model, needed to provide emissions projections and to assess an increasingly complex policy environment; a new global terrestrial model comprised of state-of-the-art biogeophysical, ecological and natural biogeochemical flux components, which provides an improved capacity to study consequences of hydrologic and ecologic change; the addition of a three-dimensional ocean representation, replacing the previous two-dimensional model, which allows examination of the global thermohaline circulation and its associated climate change impacts; the addition of an explicit oceanic carbon cycle including the impact of the biological pump; the addition of a new urban air pollution model enabling better treatments of human health and climate impacts; and the addition of greater flexibility for study of terrestrial ecosystem and urban pollution effects. This report documents the essential features of the new IGSM structure.This research was supported by the U.S Department of Energy, U.S. Environmental Protection Agency, U.S. National Science Foundation, U.S. National Aeronautics and Space Administration, U.S. National Oceanographic and Atmospheric Administration; and the Industry and Foundation Sponsors of the MIT Joint Program on the Science and Policy of Global Change: Alstom Power (France), American Electric Power (USA), BP p.l.c. (UK/USA), Chevron Corporation (USA), CONCAWE (Belgium), DaimlerChrysler AG (Germany), Duke Energy (USA), J-Power (Japan), Electric Power Research Institute (USA), Electricité de France, ExxonMobil Corporation (USA), Ford Motor Company (USA), General Motors (USA), Murphy Oil Corporation (USA), Oglethorpe Power Corporation (USA), RWE Power (Germany), Shell Petroleum (Netherlands/UK), Southern Company (USA), Statoil ASA (Norway), Tennessee Valley Authority (USA), Tokyo Electric Power Company (Japan), Total (France), G. Unger Vetlesen Foundation (USA)

Tramadolium picrate

In the title salt {systematic name: [2-hy­droxy-3-(3-meth­oxy­phen­yl)cyclo­hexyl­meth­yl]dimethyl­aza­nium 2,4,6-trinitro­phenol­ate}, C16H26NO2 +·C6H2N3O7 −, the cation is protonated at the N atom. The cyclo­hexane ring adopts a chair conformation with the hy­droxy substituent in an axial position. In the crystal, O—H⋯O and N—H⋯O hydrogen bonds link the cations and anions into supra­molecular chains along [100]

(1RS,6SR)-Ethyl 4,6-bis­(4-fluoro­phen­yl)-2-oxocyclo­hex-3-ene-1-carboxyl­ate

In the crystal structure of the title compound, C21H18F2O3, the cyclo­hexene ring has a slightly distorted sofa conformation; the two benzene rings are inclined by 76.27 (8)° and their planes make dihedral angles of 16.65 (10) and 67.53 (7)° with the approximately planar part of the cyclo­hexenone ring [maximum deviation 0.044 (2) Å, while the sixth atom is displaced by 0.648 (3) Å from this plane]. In the crystal, weak inter­molecular C—H⋯O, C—H⋯F and C—H⋯π inter­actions join mol­ecules into a three-dimensional structure

(E)-3-(4-Chloro­phen­yl)-1-(1-naphth­yl)prop-2-en-1-one

In the title compound, C19H13ClO, the benzene ring and the naphthalene system, are twisted by 12.3 (3) and 36.1 (2)°, respectively, and in opposite directions with respect to the central propenone bridge. The bond-angle pattern within the benzene ring is influence by both substituents; these influences are almost additive. In the crystal, the molecules are linked by C—H⋯O and C—H⋯Cl inter­actions

Western Pacific atmospheric nutrient deposition fluxes, their impact on surface ocean productivity

The atmospheric deposition of both macronutrients and micronutrients plays an important role in driving primary productivity, particularly in the low-latitude ocean. We report aerosol major ion measurements for five ship-based sampling campaigns in the western Pacific from similar to 25 degrees N to 20 degrees S and compare the results with those from Atlantic meridional transects (similar to 50 degrees N to 50 degrees S) with aerosols collected and analyzed in the same laboratory, allowing full incomparability. We discuss sources of the main nutrient species (nitrogen (N), phosphorus (P), and iron (Fe)) in the aerosols and their stoichiometry. Striking north-south gradients are evident over both basins with the Northern Hemisphere more impacted by terrestrial dust sources and anthropogenic emissions and the North Atlantic apparently more impacted than the North Pacific. We estimate the atmospheric supply rates of these nutrients and the potential impact of the atmospheric deposition on the tropical western Pacific. Our results suggest that the atmospheric deposition is P deficient relative to the needs of the resident phytoplankton. These findings suggest that atmospheric supply of N, Fe, and P increases primary productivity utilizing some of the residual excess phosphorus (P*) in the surface waters to compensate for aerosol P deficiency. Regional primary productivity is further enhanced via the stimulation of nitrogen fixation fuelled by the residual atmospheric iron and P*. Our stoichiometric calculations reveal that a P* of 0.1 mu mol L-1 can offset the P deficiency in atmospheric supply for many months. This study suggests that atmospheric deposition may sustain similar to 10% of primary production in both the western tropical Pacific

2-(4-Methoxy­phen­yl)-6-trifluoro­methyl-1H-pyrrolo[3,2-c]quinoline monohydrate

In the title compound, C19H13F3N2O·H2O, the phenyl and pyrroloquinoline ring system are close to coplanar [dihedral angle = 10.94 (4)°]. The meth­oxy group also is almost coplanar with the phenyl ring [5.4 (1)°]. In the crystal structure N—H⋯O(water) and water–quinoline O—H⋯N hydrogen bonds build up a supra­molecular chain-like arrangement along [001]. The remaining H atom of the water mol­ecule does not take part in classical hydrogen bonds. Instead, this O—H bond points toward the center of the phenyl ring of a neighbouring mol­ecule. Weak C—H⋯O and C—H⋯π inter­actions are also present