The title compounds, [Mo(C5H5)(COCH3)(C6H12N3P)(CO)2], (1), and [Mo(C5H5)(COCH3)(C9H16N3O2P)(C6H5)2))(CO)2], (2), have been prepared by phosphine-induced migratory insertion from [Mo(C5H5)(CO)3(CH3)]. The mol­ecular structures of these complexes are quite similar, exhibiting a four-legged piano-stool geometry with trans-disposed carbonyl ligands. The extended structures of complexes (1) and (2) differ substanti­ally. For complex (1), the molybdenum acetyl unit plays a dominant role in the organization of the extended structure, joining the mol­ecules into centrosymmetrical dimers through C—H⋯O inter­actions with a cyclo­penta­dienyl ligand of a neighboring mol­ecule, and these dimers are linked into layers parallel to (100) by C—H⋯O inter­actions between the molybdenum acetyl and the cyclo­penta­dienyl ligand of another neighbor. The extended structure of (2) is dominated by C—H⋯O inter­actions involving the carbonyl groups of the acetamide groups of the DAPTA ligand, which join the mol­ecules into centrosymmetrical dimers and link them into chains along [010]. Additional C—H⋯O inter­actions between the molybdenum acetyl oxygen atom and an acetamide methyl group join the chains into layers parallel to (101).

The title compound, bis­(1,2-diphenyl-2-sulfanyl­idene­ethane­thiol­ato-κ2S,S')(1,3,5-tri­aza-7-phosphaadamantane-κP)cobalt(II) dichloromethane hemisolvate, [Co(pdt)2(PTA)]·0.5C2H4Cl2 or [Co(C14H10S2)2(C6H12N3P)]·0.5C2H4Cl2, contains two phenyl­dithiol­ene (pdt) ligands and a 1,3,5-tri­aza-7-phosphaadamantane (PTA) ligand bound to cobalt with the solvent 1,2-di­chloro­ethane mol­ecule located on an inversion center. The cobalt core exhibits an approximately square-pyramidal geometry with partially reduced thienyl radical monoanionic ligands. The supra­molecular network is consolidated by hydrogen-bonding inter­actions primarily with nitro­gen, sulfur and chlorine atoms, as well as parallel displaced π-stacking of the aryl rings. The UV–vis, IR, and CV data are also consistent with monoanionic di­thiol­ene ligands and an overall CoII oxidation state.

The mechanism of formation of residual strain in crystals with a damaged surface has been studied by transmission electron microscopy in GaAs wafers ground with sandpaper. The samples showed a dislocation network located near the sample surface penetrating to a depth of a few micrometres, comparable to the size of abrasive particles used for the treatment, and no other types of defects were observed. A simple model for the formation of a compressive strain induced by the dislocation network in the damaged layer is proposed, in satisfactory agreement with the measured strain. The strain is generated by the formation of dislocation half-loops at the crystal surface, having the same component of the Burgers vectors parallel to the surface of the crystal. This is equivalent to the insertion of extra half-planes from the crystal surface to the depth of the damaged zone. This model can be generalized for other crystal structures. An approximate calculation of the strain generated from the observed dislocation distribution in the sample agrees with the proposed model and permits the conclusion that this mechanism is in general sufficient to explain the observed compressive strain, without the need to consider other types of defects.

Traditionally small-molecule crystallographers have not usually observed or recognized significant radiation damage to their samples during diffraction experiments. However, the increased flux densities provided by third-generation synchrotrons have resulted in increasing numbers of observations of this phenomenon. The diversity of types of small-molecule systems means it is not yet possible to propose a general mechanism for their radiation-induced sample decay, however characterization of the effects will permit attempts to understand and mitigate it. Here, systematic experiments are reported on the effects that sample temperature and beam attenuation have on radiation damage progression, allowing qualitative and quantitative assessment of their impact on crystals of a small-molecule test sample. To allow inter-comparison of different measurements, radiation-damage metrics (diffraction-intensity decline, resolution fall-off, scaling B-factor increase) are plotted against the absorbed dose. For ease-of-dose calculations, the software developed for protein crystallography, RADDOSE-3D, has been modified for use in small-molecule crystallography. It is intended that these initial experiments will assist in establishing protocols for small-molecule crystallographers to optimize the diffraction signal from their samples prior to the onset of the deleterious effects of radiation damage.

Copper-containing nitrite reductases (CuNiRs) that convert NO2− to NO via a CuCAT–His–Cys–CuET proton-coupled redox system are of central importance in nitrogen-based energy metabolism. These metalloenzymes, like all redox enzymes, are very susceptible to radiation damage from the intense synchrotron-radiation X-rays that are used to obtain structures at high resolution. Understanding the chemistry that underpins the enzyme mechanisms in these systems requires resolutions of better than 2 Å. Here, for the first time, the damage-free structure of the resting state of one of the most studied CuNiRs was obtained by combining X-ray free-electron laser (XFEL) and neutron crystallography. This represents the first direct comparison of neutron and XFEL structural data for any protein. In addition, damage-free structures of the reduced and nitrite-bound forms have been obtained to high resolution from cryogenically maintained crystals by XFEL crystallography. It is demonstrated that AspCAT and HisCAT are deprotonated in the resting state of CuNiRs at pH values close to the optimum for activity. A bridging neutral water (D2O) is positioned with one deuteron directed towards AspCAT Oδ1 and one towards HisCAT N∊2. The catalytic T2Cu-ligated water (W1) can clearly be modelled as a neutral D2O molecule as opposed to D3O+ or OD−, which have previously been suggested as possible alternatives. The bridging water restricts the movement of the unprotonated AspCAT and is too distant to form a hydrogen bond to the O atom of the bound nitrite that interacts with AspCAT. Upon the binding of NO2− a proton is transferred from the bridging water to the Oδ2 atom of AspCAT, prompting electron transfer from T1Cu to T2Cu and reducing the catalytic redox centre. This triggers the transfer of a proton from AspCAT to the bound nitrite, enabling the reaction to proceed.

The local Fourier-space relation between diffracted intensity I, diffraction wavevector q and dose D, ilde I(q,D), is key to probing and understanding radiation damage by X-rays and energetic particles in both diffraction and imaging experiments. The models used in protein crystallography for the last 50 years provide good fits to experimental I(q) versus nominal dose data, but have unclear physical significance. More recently, a fit to diffraction and imaging experiments suggested that the maximum tolerable dose varies as q−1 or linearly with resolution. Here, it is shown that crystallographic data have been strongly perturbed by the effects of spatially nonuniform crystal irradiation and diffraction during data collection. Reanalysis shows that these data are consistent with a purely exponential local dose dependence, ilde I(q,D) = I0(q)exp[−D/De(q)], where De(q) ∝ qα with α ≃ 1.7. A physics-based model for radiation damage, in which damage events occurring at random locations within a sample each cause energy deposition and blurring of the electron density within a small volume, predicts this exponential variation with dose for all q values and a decay exponent α ≃ 2 in two and three dimensions, roughly consistent with both diffraction and imaging experiments over more than two orders of magnitude in resolution. The B-factor model used to account for radiation damage in crystallographic scaling programs is consistent with α = 2, but may not accurately capture the dose dependencies of structure factors under typical nonuniform illumination conditions. The strong q dependence of radiation-induced diffraction decays implies that the previously proposed 20–30 MGy dose limit for protein crystallography should be replaced by a resolution-dependent dose limit that, for atomic resolution data sets, will be much smaller. The results suggest that the physics underlying basic experimental trends in radiation damage at T ≃ 100 K is straightforward and universal. Deviations of the local I(q, D) from strictly exponential behavior may provide mechanistic insights, especially into the radiation-damage processes responsible for the greatly increased radiation sensitivity observed at T ≃ 300 K.

Each year thousands of vacationers enjoy the scenery along Virginia’s Skyline Drive, little knowing that for a few brief moments they are passing through the territory of an endangered […]

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The fossil teeth of a 15- to 18-million-year-old three-toed browsing horse, Anchitherium clarencei, were recently discovered by scientists from the Smithsonian Tropical Research Institute and the […]

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A new census of tropical sulfur butterflies (Aphrissa statira) migrating across the Panama Canal has revealed the central role that weather plays in determining why populations of these lemon-yellow insects vary from year to year.

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The newfound world, GJ1214b, is about 6.5 times as massive as the Earth. Its host star, GJ1214, is a small, red type M star about one-fifth the size of the Sun. GJ1214b orbits its star once every 38 hours at a distance of only 1.3 million miles. Astronomers estimate the planet's temperature to be about 400 degrees Fahrenheit. Although warm as an oven, it is still cooler than any other known transiting planet because it orbits a very dim star.

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The rescue pods will be part of the project’s Amphibian Rescue Center at Summit Municipal Park, which will also include a lab with a quarantine facility.

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“We are working as hard as we can to find and identify frogs before the disease reaches them, and to learn more about a disease that has the power to ravage an entire group of organisms,” said Roberto Ibanez, research scientist at STRI and local director of the Panama Amphibian Rescue and Conservation Project.

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The Smithsonian’s National Zoo recently acquired Japanese giant salamanders given to the Zoo by the City of Hiroshima Asa Zoological Park. This donation will be the foundation of a new long-term breeding program in the United States and may play an important role in saving amphibians around the globe.

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Discoveries of three new from species in Panama lead to hope that project researchers can save these animals from a deadly fungus killing frogs worldwide and the fear that many species will go extinct before scientists even know they exist.

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Scientists and local dive operators first noticed coral bleaching in the waters surrounding Isla Colon, in Panama’s Bocas del Toro province in July. Smithsonian staff scientist Nancy Knowlton and colleagues documented an extensive bleaching event in late September.

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The National Zoo’s great cat program recently expanded with the arrival of two-and-a-half-year-old female Sumatran tiger, Damai, who is now out of quarantine and spending time outside in her exhibit where visitors can see her.

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A scientist from the Smithsonian Tropical Research Institute uses a pick to dislodge the fossil skull of an extinct toothed whale from sediments on the […]

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The 5.8-magnitude earthquake that shook the eastern United States on the afternoon of Tuesday, Aug. 23, caused minor damage to some of the Smithsonian's natural history collections. All public Smithsonian museums are open and have been determined safe for visitors and staff.

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Two scientists at the Smithsonian Institution have been honored with the Presidential Early Career Award for Scientists and Engineers for their innovative research and scientific leadership. It is the highest honor bestowed by the U.S. government on science and engineering professionals in the early stages of their independent research careers.

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Our studies of the genetic relationships between these bees tells us that they originated in the Amazon about 22 million years ago and that they moved north into Central America before 3 million years ago.

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Smithsonian Secretary Wayne Clough, left, talks with Carlos Jaramillo, scientist at the Smithsonian Tropical Research Institute in Panama, at a research site near the Panama […]

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The discovery of two new extinct camel species by scientists from the University of Florida and the Smithsonian is casting new light on the history of the tropics, a region containing more than half the world's biodiversity and some of its most important ecosystems.

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The newly reported reconstruction of Amazonian prehistory by a Smithsonian scientist, Dolores R. Piperno, and her colleagues suggests that large areas of western Amazonia were sparsely inhabited.

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Researchers from the Smithsonian Tropical Research Institute are recommending that Panama adopt revised traffic patterns and slower speeds for vessels crossing the Gulf of Panama to reduce the risk of collisions between ships and whales.

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A specimen recently pulled from deep in the southwest Atlantic may represent a new species of squid, say scientist who have studied the animal’s unusual morphology. But then again, it may not…

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This past summer, Laura Walker became the first scientist to collect slime molds from soils at the Barro Colorado Nature Monument in Panama, a reserve administered by the Smithsonain since 1946.

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Archaeologists working at the Smithsonian Tropical Research Institute in Panama have discovered a cluster of 12 unusual stones in the back of a small, prehistoric rock-shelter near the town of Boquete.

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A team of researchers has for the first time mapped the above ground carbon density of an entire country in high fidelity. They integrated field […]

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The Panama Amphibian Rescue and Conservation project recently announced that the golden frog, a national icon on the brink of extinction, has been successfully raised […]

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The Republic of Panama’s proposal to implement four Traffic Separation Schemes for commercial vessels entering and exiting the Panama Canal and ports was approved unanimously […]

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The name Panama is said to mean “abundance of fish.” Now a new study estimates that between 1950 and 2010, the amount of fish taken […]

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Human skin and gut microbes influence processes from digestion to disease resistance. Despite the fact that tropical forests are the most biodiverse terrestrial ecosystems on […]

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A bright orange poison dart frog with a unique call was discovered in Donoso, Panama, and described by researchers from the Smithsonian Tropical Research Instituteand […]

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What do you want to be when you grow up? Would you want to explore the world searching for long lost creatures of our past? […]

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From bizarre bugs to penis spines on bats, our world is infinitely expanded when we look down the microscope! Check out the stories behind these […]

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More than two million migrating raptors passed over Panama City on Sunday, Nov. 2, doubling the previous record of almost 900,000 tallied in a single […]

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Salamanders are typically elusive animals and adept at hiding, but National Zoo visitors will have a chance to see a variety of different amphibian species […]

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The bush dog is one of the most enigmatic of the world’s canid species, seldom seen throughout its range in Central and South America. New […]

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For the past 50 years, the number of wood thrush (Hylocichla mustelina) that breed in the United States has decreased more than 60 percent. However, […]

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Cobia, a promising fish for aquaculture, lives throughout the world’s oceans except in the Central and Eastern Pacific. In August 2015, a large number of […]

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Seven fossil teeth exposed by the Panama Canal expansion project are the first evidence of a monkey on the North American continent before the Isthmus […]

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Ricardo Moreno, research associate at the Smithsonian Tropical Research Institute (STRI) in Panama and director of the Yaguará Panamá Foundation, reported at the 20th Congress […]

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In 1969, 60 to 100 peacock bass imported from Buga, Colombia, were introduced into a pond in Panama for sport fishing. Several individuals escaped. By […]

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Ninety Limosa harlequin frogs (Atelopus limosus) bred in human care are braving the elements of the wild after Smithsonian scientists sent them out into the […]

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This user-friendly, portable, and extensive identification guide features large color illustrations of more than 900 species; the first range maps published to show the distribution of Panama's birds and concise text that describes field marks for identification, as well as habitat, behavior, and vocalizations.

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Imke K. Mandemaker, Di Zhou, Serena T. Bruens, Dick H. Dekkers, Pernette J. Verschure, Raghu R. Edupuganti, Eran Meshorer, Jeroen A. Demmers, and Jurgen A. Marteijn

Many chromatin remodeling and modifying proteins are involved in the DNA damage response by stimulating repair or inducing DNA damage signaling. Interestingly, here we identified that down regulation of the H1-interacting protein SET results in increased resistance to a wide variety of DNA damaging agents. We found that this increased resistance is not the result of an inhibitory effect of SET on DNA repair, but rather the consequence of a suppressed apoptotic response to DNA damage. We further provide evidence that the histone chaperone SET is responsible for the eviction of H1 from chromatin. Knock down of H1 in SET-depleted cells resulted in re-sensitization of cells to DNA damage, suggesting that the increased DNA damage resistance in SET-depleted cells is the result of enhanced retention of H1 on chromatin. Finally, clonogenic survival assays show that SET and p53 are epistatic in attenuating DNA damage-induced cell death. Altogether, our data show a role for SET in the DNA damage response as a regulator of cell survival following genotoxic stress.

To understand the long-term effects of a prolonged tropical storm in the Panama Canal watershed, Robert Stallard, staff scientist at the Smithsonian Tropical Research Institute and research hydrologist at the U.S. Geological Survey, and Armando Ubeda, the LightHawk Mesoamerica program manager, organized four flights over the watershed to create a digital map of landslide scars.

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The National Museum of Natural History will permanently display the Dom Pedro Aquamarine, which is the largest single piece of cut-gem aquamarine in the world, beginning Dec. 6.

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The humble salamander may provide evidence to support a controversial claim that North and South America were joined together much earlier than previously thought. The […]

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Miniature camels and horses, a rhinoceros and a giant bear-dog are among fossils unearthed in the recent excavations of the Panama Canal expansion project. These […]

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