This Earth Day weekend in Washington, D.C., the Smithsonian is convening the first Earth Optimism Summit. The three-day event, taking place April 21–23, will look […]

The post Earth Optimism: Smithsonian’s “Agua Salud” Project restores degraded land with forest appeared first on Smithsonian Insider.

If you’ve seen the movie Jurassic Park, you know that amber played a significant role in rebuilding a lost world: A mosquito trapped within its […]

The post Resin from shipwreck hints at trade routes and botany of ancient Asia appeared first on Smithsonian Insider.

Zebra mussels in the Great Lakes, lionfish in the Atlantic and pythons in the Everglades: Large creatures like these generally draw the spotlight when talking […]

The post DNA is trusty new weapon for detecting slime nets and other invasive marine parasites appeared first on Smithsonian Insider.

A tiny invasive insect from Asia might have an effect on Chesapeake Bay waters. The emerald ash borer is killing millions of ash trees in […]

The post Invasive ash borer found in Smithsonian Environmental Research Center forest; ash deaths may impact Chesapeake waters appeared first on Smithsonian Insider.

Hidden in plain sight–that’s how researchers describe their discovery of a new genus of large forest tree commonly found, yet previously scientifically unknown, in the […]

The post Remarkable new tree species was “hidden in plain sight” in the Andes appeared first on Smithsonian Insider.

White-tailed deer don’t like to eat the invasive plants Japanese stilt grass, garlic mustard or barberry. Native oak seedlings and tulip poplar, on the other […]

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“One cannot think well, love well, sleep well if one has not dined well,” Virginia Woolf once said. Woolf’s sentiment is one that the staff […]

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No green thumb? You don’t need to water these dazzling orchids to enjoy them. More than 8,000 living specimens in the Smithsonian Gardens Orchid Collection […]

The post See thousands of orchids in incredible detail in the Smithsonian’s newly digitized collection appeared first on Smithsonian Insider.

This article aims to encourage practitioners, young and seasoned, by enhancing their structure-determination toolboxes with a selection of tips and tricks on recognizing and handling aspects of data collection, structure modelling and refinement, and the interpretation of results.

In the first reported crystal structure involving the potential ligand N,N',N''-tris­(2-pyridin­yl)-1,3,5-benzene­tricarboxamide, inter­molecular N—H⋯O hydrogen bonds link the mol­ecules via their amide groups into slanted ladder-like chains. Only two of the three amide groups in the mol­ecule are involved in hydrogen bonding, which influences the degree of out-of-plane twisting at each amide group.

The crystal structure of vanthoffite, Na6Mg(SO4)4, was redetermined and refined with anisotropic displacement parameters for all atoms. Here, for the first time, we give its detailed description.

The new copper(II) complex [CuLCl2]2, where L is a product of Schiff base condensation between methyl­amine and 2-pyridine­carbaldehyde, is built of discrete centrosymmetric dimers.

This work presents a technique for extracting the detailed shape of peaks with extended, overlapping tails in an X-ray powder diffraction pattern. The application discussed here concerns crystallite size broadening, though the technique can be applied to spectra of any origin and without regard to how the profiles are to be subsequently analyzed. Historically, the extraction of profile shapes has been difficult due to the complexity of determining the background under the peak, resulting in an offset of the low-frequency components of the Fourier transform of the peak known as the `hook' problem. The use of a carefully considered statistical weighting function in a non-linear least-squares fit, followed by summing the residuals from such a fit with the fit itself, allows one to extract the full shape of an isolated peak, without contributions from either the background or adjacent peaks. The extracted shape, consisting of the fit function recombined with the residuals, is not dependent on any specific shape model. The application of this to analysis of microstructure is performed independently of global parametric models, which would reduce the number of refined parameters; therefore the technique requires high-quality data to produce results of interest. The effectiveness of the technique is demonstrated by extraction of Fourier transforms of peaks from two sets of size-broadened materials with two differing pieces of equipment.

It is shown how to reconstruct the stacking sequence from the pairwise correlation functions between layers in close-packed structures. First, of theoretical interest, the analytical formulation and solution of the problem are presented when the exact pairwise correlation counts are known. In the second part, the practical problem is approached. A simulated annealing procedure is developed to solve the problem using as initial guess approximate solutions from previous treatments. The robustness of the procedure is tested with synthetic data, followed by an experimental example. The developed approach performs robustly over different synthetic and experimental data, comparing favorably with the reported methods.

The methods for X-ray crystal orientation are rapidly evolving towards versatility, fewer goniometry measurements, automation, high accuracy and precision. One method that attracts a lot of attention is energy-dispersive X-ray diffraction (EDXRD) which is based on detecting reflections from crystallographic planes in a crystal at fixed angles of a parallel polychromatic X-ray incident beam. In theory, an EDXRD peak can move in a diffraction pattern as a function of a crystallographic plane d-spacing and its orientation relative to a fixed direction in space can change also. This is equivalent to the possibility of measuring the orientation of single crystals. The article provides a modeling for the EDXRD method whose main feature is the nonmoving crystal in the sense of traditional goniometry where the angle measurements of diffracting planes are a must. The article defines the equation of orientation for the method and shows the derivation in great detail. It is shown that the exact solutions of the equations can be obtained using the generalized reduced gradient method, a mathematical subroutine that is implemented in Excel software. The significance and scientific impact of the work are discussed along with the validated tested results.

A new aspherical scattering factor formalism has been implemented in the crystallographic least-squares refinement program SHELXL. The formalism relies on Gaussian functions and can optionally complement the independent atom model to take into account the deformation of electron-density distribution due to chemical bonding and lone pairs. Asphericity contributions were derived from the electron density obtained from quantum-chemical density functional theory computations of suitable model compounds that contain particular chemical environments, as defined by the invariom formalism. Thanks to a new algorithm, invariom assignment for refinement in SHELXL is automated. A suitable parameterization for each chemical environment within the new model was achieved by metaheuristics. Figures of merit, precision and accuracy of crystallographic least-squares refinements improve significantly upon using the new model.

To date X-ray protein crystallography is the most successful technique available for the determination of high-resolution 3D structures of biological molecules and their complexes. In X-ray protein crystallography the structure of a protein is refined against the set of observed Bragg reflections from a protein crystal. The resolution of the refined protein structure is limited by the highest angle at which Bragg reflections can be observed. In addition, the Bragg reflections alone are typically insufficient (by a factor of two) to determine the structure ab initio, and so prior information is required. Crystals formed from an imperfect packing of the protein molecules may also exhibit continuous diffraction between and beyond these Bragg reflections. When this is due to random displacements of the molecules from each crystal lattice site, the continuous diffraction provides the necessary information to determine the protein structure without prior knowledge, to a resolution that is not limited by the angular extent of the observed Bragg reflections but instead by that of the diffraction as a whole. This article presents an iterative projection algorithm that simultaneously uses the continuous diffraction as well as the Bragg reflections for the determination of protein structures. The viability of this method is demonstrated on simulated crystal diffraction.

Diffuse scattering is a rich source of information about disorder in crystalline materials, which can be modelled using atomistic techniques such as Monte Carlo and molecular dynamics simulations. Modern X-ray and neutron scattering instruments can rapidly measure large volumes of diffuse-scattering data. Unfortunately, current algorithms for atomistic diffuse-scattering calculations are too slow to model large data sets completely, because the fast Fourier transform (FFT) algorithm has long been considered unsuitable for such calculations [Butler & Welberry (1992). J. Appl. Cryst. 25, 391–399]. Here, a new approach is presented for ultrafast calculation of atomistic diffuse-scattering patterns. It is shown that the FFT can actually be used to perform such calculations rapidly, and that a fast method based on sampling theory can be used to reduce high-frequency noise in the calculations. These algorithms are benchmarked using realistic examples of compositional, magnetic and displacive disorder. They accelerate the calculations by a factor of at least 102, making refinement of atomistic models to large diffuse-scattering volumes practical.

In a Model block, if the instance-specific value of a model argument has an anonymous structure type, an update diagram reports an error when there are multiple bus types that match that anonymous structure type.This bug exists in the following release(s):
R2020a

This bug has a workaround

Interested in Upgrading?

Attempting to display the contents of an HDF5 file containing fixed-length UTF-8 encoded strings results in an unexpected error in MATLAB.

For example, the following code

  h5disp('myHDF5FileWithFixedLenUTF8Strings.h5')

returns this error:

Error using h5infoc
UTF-8 encoding is only supported for variable length strings.

Error in h5info (line 108)
hinfo = h5infoc(filename,location, useUtf8);

Error in h5disp>display_hdf5 (line 121)
hinfo = h5info(options.Filename,options.Location);

Error in h5disp (line 99)
display_hdf5(options);

Simulink might produce an incorrect sorted order for a model that meets all of the following conditions:

• The model contains blocks from the SoC Blockset
• The Signal logging option is selected in the model configuration set
• Signals using asynchronous sample time are configured for logging

For several versions of Windows

Customers online want convenience, ease, and access. Fortunately, your business offers it all. Unfortunately, thats what fraudsters want too.

The new Cross-Border Payments and Commerce Report 2019 – 2020 depicts the major trends driving growth in cross-border payments, cross-border commerce, and marketplaces.

Who’s Who in Payments – Complete Overview of Key Payment Providers encompasses key trends in the payments industry.

The GDC Compliance Advisory Board (CAB) provides insight into how to interpret the Strong Consumer Authentication (SCA) mandate described in PSD 2 without jeopardizing data privacy concerns protected by GDPR. 

The new copper(II) complex, namely, di-μ-chlorido-bis{chlorido[methyl(pyridin-2-ylmethylidene)amine-κ2N,N']copper(II)}, [Cu2Cl4(C7H8N2)2], (I), with the ligand 2-pyridylmethyl-N-methylimine (L, a product of Schiff base condensation between methylamine and 2-pyridinecarbaldehyde) is built of discrete centrosymmetric dimers. The coordination about the CuII ion can be described as distorted square pyramidal. The base of the pyramid consists of two nitrogen atoms from the bidentate chelate L [Cu—N = 2.0241 (9), 2.0374 (8) Å] and two chlorine atoms [Cu—Cl = 2.2500 (3), 2.2835 (3) Å]. The apical position is occupied by another Cl atom with the apical bond being significantly elongated at 2.6112 (3) Å. The trans angles of the base are 155.16 (3) and 173.79 (2)°. The Cu...Cu separation in the dimer is 3.4346 (3) Å. In the crystal structure, the loosely packed dimers are arranged in stacks propagating along the a axis. The X-band polycrystalline 77 K EPR spectrum of (I) demonstrates a typical axial pattern characteristic of mononuclear CuII complexes. Compound (I) is redox active and shows a cyclic voltammetric response with E1/2 = −0.037 V versus silver–silver chloride electrode (SSCE) assignable to the reduction peak of CuII/CuI in methanol as solvent.

The crystal structure of vanthoffite {hexasodium magnesium tetrakis[sulfate(VI)]}, Na6Mg(SO4)4, was solved in the year 1964 on a synthetic sample [Fischer & Hellner (1964). Acta Cryst. 17, 1613]. Here we report a redetermination of its crystal structure on a mineral sample with improved precision. It was refined in the space group P21/c from a crystal originating from Surtsey, Iceland. The unique Mg (site symmetry overline{1}) and the two S atoms are in usual, only slightly distorted octahedral and tetrahedral coordinations, respectively. The three independent Na atoms are in a distorted octahedral coordination (1×) and distorted 7-coordinations intermediate between a `split octahedron' and a pentagonal bipyramid (2×). [MgO6] coordination polyhedra interchange with one half of the sulfate tetrahedra in <011> chains forming a (100) meshed layer, with dimers formed by edge-sharing [NaO7] polyhedra filling the interchain spaces. The other [NaO7] polyhedra are organized in a parallel layer formed by [010] and [001] chains united through edge sharing and bonds to the remaining half of sulfate groups and to [NaO6] octahedra. The two types of layers interconnect through tight bonding, which explains the lack of morphological characteristics typical of layered structures.

In the first reported crystal structure involving the potential ligand N,N',N''-tris(pyridin-2-yl)benzene-1,3,5-tricarboxamide, C24H18N6O3, intermolecular N—H...O hydrogen bonds link the molecules via their amide groups into slanted ladder-like chains, in which the uprights of the ladder are formed by the hydrogen-bonding interactions and the benzene ring cores of the molecules act as the rungs of the ladder. Only two of the three amide groups in the molecule are involved in hydrogen bonding and this influences the degree of out-of-plane twisting at each amide group, with the twist being more significant for those amide groups participating in hydrogen bonds.

In small-molecule single-crystal structure determination, we now have at our disposal an inspiring range of fantastic diffractometers with better, brighter sources, and faster, more sensitive detectors. Faster and more powerful computers provide integrated tools and software with impressive graphical user interfaces. Yet these tools can lead to the temptation not to check the work thoroughly and one can too easily overlook tell-tale signs that something might be amiss in a structure determination; validation with checkCIF is not always revealing. This article aims to encourage practitioners, young and seasoned, by enhancing their structure-determination toolboxes with a selection tips and tricks on recognizing and handling aspects that one should constantly be aware of. Topics include a pitfall when setting up data collections, the usefulness of reciprocal lattice layer images, processing twinned data, tips for disorder modelling and the use of restraints, ensuring hydrogen atoms are added to a model correctly, validation beyond checkCIF, and the derivation and interpretation of the final results.