'Surrey swarm' earthquakes not caused by nearby oil extraction, study suggests  Science Daily

Climate change: Cardiff study says ground-water could heat homes  BBC News

Rice AKR in the apo structure reveals the ordered open conformation and its key residues which form the substrate channel wall and determine its substrate preference for straight-chain aldehydes.

The title Schiff base compound, C13H9ClN4O5·0.5CH3CN, crystallizes as an aceto­nitrile hemisolvate; the solvent mol­ecule being located on a twofold rotation axis. The mol­ecule is nearly planar, with a dihedral angle between the two benzene rings of 3.7 (2)°. The configuration about the C=N bond is E, and there is an intra­molecular N—H⋯Onitro hydrogen bond present forming an S(6) ring motif. In the crystal, mol­ecules are linked by O—H⋯O and N—H⋯O hydrogen bonds, forming layers lying parallel to (10overline{1}). The layers are linked by C—H⋯Cl hydrogen bonds, forming a supra­molecular framework. Within the framework there are offset π–π stacking inter­actions [inter­centroid distance = 3.833 (2) Å] present involving inversion-related mol­ecules. The DFT study shows that the HOMO and LUMO are localized in the plane extending from the phenol ring to the 2,4-di­nitro­benzene ring, and the HOMO–LUMO gap is found to be 0.13061 a.u.

In the title quinoline derivative, C14H14ClNO3, there is an intra­molecular C—H⋯O hydrogen bond forming an S(6) graph-set motif. The mol­ecule is essentially planar with the mean plane of the ethyl acetate group making a dihedral angle of 5.02 (3)° with the ethyl 6-chloro-2-eth­oxy­quinoline mean plane. In the crystal, offset π–π inter­actions with a centroid-to-centroid distance of 3.4731 (14) Å link inversion-related mol­ecules into columns along the c-axis direction. Hirshfeld surface analysis indicates that H⋯H contacts make the largest contribution (50.8%) to the Hirshfeld surface.

In the title quinoline derivative, C24H19NO3, the two benzyl rings are inclined to the quinoline ring mean plane by 74.09 (8) and 89.43 (7)°, and to each other by 63.97 (10)°. The carboxyl­ate group is twisted from the quinoline ring mean plane by 32.2 (2)°. There is a short intra­molecular C—H⋯O contact forming an S(6) ring motif. In the crystal, mol­ecules are linked by bifurcated C—H,H⋯O hydrogen bonds, forming layers parallel to the ac plane. The layers are linked by C—H⋯π inter­actions, forming a supra­molecular three-dimensional structure.

The asymmetric unit of the title compound, C15H12N2O2, contains two crystallographically independent mol­ecules in which the dihedral angles between the benzene rings in each are 13.26 (5) and 7.87 (5)°. An intra­molecular O—H⋯N hydrogen bonds results in the formation of an S(6) ring motif. In the crystal, mol­ecules are linked by weak C—H⋯O and C—H⋯N hydrogen bonds, forming layers parallel to (011). In addition, π–π stacking inter­actions with centroid–centroid distances in the range 3.693 (2)–3.931 (2) Å complete the three-dimensional network.

The title pyridazin-3(2H)-one derivative, C25H19FN2O2, crystallizes with two independent mol­ecules (A and B) in the asymmetric unit. In mol­ecule A, the 4-fluoro­phenyl ring, the benzyl ring and the phenyl ring are inclined to the central pyridazine ring by 86.54 (11), 3.70 (9) and 84.857 (13)°, respectively. In mol­ecule B, the corresponding dihedral angles are 86.80 (9), 10.47 (8) and 82.01 (10)°, respectively. In the crystal, the A mol­ecules are linked by pairs of C—H⋯F hydrogen bonds, forming inversion dimers with an R22(28) ring motif. The dimers are linked by C—H⋯O hydrogen bonds and a C—H⋯π inter­action, forming columns stacking along the a-axis direction. The B mol­ecules are linked to each other in a similar manner and form columns separating the columns of A mol­ecules.

The asymmetric unit of the title 1:1 solvate, C14H14N4O2·C6H6 [systematic name of the oxalamide mol­ecule: N,N'-bis­(pyridin-4-ylmeth­yl)ethanedi­amide], comprises a half mol­ecule of each constituent as each is disposed about a centre of inversion. In the oxalamide mol­ecule, the central C2N2O2 atoms are planar (r.m.s. deviation = 0.0006 Å). An intra­molecular amide-N—H⋯O(amide) hydrogen bond is evident, which gives rise to an S(5) loop. Overall, the mol­ecule adopts an anti­periplanar disposition of the pyridyl rings, and an orthogonal relationship is evident between the central plane and each terminal pyridyl ring [dihedral angle = 86.89 (3)°]. In the crystal, supra­molecular layers parallel to (10overline{2}) are generated owing the formation of amide-N—H⋯N(pyrid­yl) hydrogen bonds. The layers stack encompassing benzene mol­ecules which provide the links between layers via methyl­ene-C—H⋯π(benzene) and benzene-C—H⋯π(pyrid­yl) inter­actions. The specified contacts are indicated in an analysis of the calculated Hirshfeld surfaces. The energy of stabilization provided by the conventional hydrogen bonding (approximately 40 kJ mol−1; electrostatic forces) is just over double that by the C—H⋯π contacts (dispersion forces).

In the title mol­ecule, C17H23NO2, the di­hydro­indole portion is planar (r.m.s. deviation = 0.0157 Å) and the nonyl substituent is in an `extended' conformation. In the crystal, the nonyl chains inter­calate and the di­hydro­indole­dione units are associated through C—H⋯O hydrogen bonds to form micellar blocks. Based on the Hirshfeld surface analysis, the most important inter­molecular inter­action is the H⋯H inter­action.

In the title compound, C27H30N4O6·H2O, the two dioxolo rings are in envelope conformations, while the pyran ring is in a twisted-boat conformation. The pyradizine ring is oriented at dihedral angles of 9.23 (6) and 12.98 (9)° with respect to the pyridine rings, while the dihedral angle between the two pyridine rings is 13.45 (10)°. In the crystal, O—Hwater⋯Opyran, O—Hwater⋯Ometh­oxy­meth­yl and O—Hwater⋯Npyridazine hydrogen bonds link the mol­ecules into chains along [010]. In addition, weak C—Hdioxolo⋯Odioxolo hydrogen bonds and a weak C—Hmeth­oxy­meth­yl⋯π inter­action complete the three-dimensional structure. The Hirshfeld surface analysis of the crystal structure indicates that the most important contributions for the crystal packing are from H⋯H (55.7%), H⋯C/C⋯H (14.6%), H⋯O/O⋯H (14.5%) and H⋯N/N⋯H (9.6%) inter­actions. Hydrogen-bonding and van der Waals inter­actions are the dominant inter­actions in the crystal packing. Electrochemical measurements are also reported.

The di-substituted acetyl­ene residue in the title compound, C11H11NO3, is capped at either end by di-methyl­hydroxy and 4-nitro­benzene groups; the nitro substituent is close to co-planar with the ring to which it is attached [dihedral angle = 9.4 (3)°]. The most prominent feature of the mol­ecular packing is the formation, via hy­droxy-O—H⋯O(hy­droxy) hydrogen bonds, of hexa­meric clusters about a site of symmetry overline{3}. The aggregates are sustained by 12-membered {⋯OH}6 synthons and have the shape of a flattened chair. The clusters are connected into a three-dimensional architecture by benzene-C—H⋯O(nitro) inter­actions, involving both nitro-O atoms. The aforementioned inter­actions are readily identified in the calculated Hirshfeld surface. Computational chemistry indicates there is a significant energy, primarily electrostatic in nature, associated with the hy­droxy-O—H⋯O(hy­droxy) hydrogen bonds. Dispersion forces are more important in the other identified but, weaker inter­molecular contacts.

The title Schiff base compound, C14H10Cl2N2O, features an E configuration about each of the C=N imine bonds. Overall, the mol­ecule is approximately planar with the dihedral angle between the central C2N2 residue (r.m.s. deviation = 0.0371 Å) and the peripheral hy­droxy­benzene and chloro­benzene rings being 4.9 (3) and 7.5 (3)°, respectively. Nevertheless, a small twist is evident about the central N—N bond [the C—N—N—C torsion angle = −172.7 (2)°]. An intra­molecular hy­droxy-O—H⋯N(imine) hydrogen bond closes an S(6) loop. In the crystal, π–π stacking inter­actions between hy­droxy- and chloro­benzene rings [inter-centroid separation = 3.6939 (13) Å] lead to a helical supra­molecular chain propagating along the b-axis direction; the chains pack without directional inter­actions between them. The calculated Hirshfeld surfaces point to the importance of H⋯H and Cl⋯H/H⋯Cl contacts to the overall surface, each contributing approximately 29% of all contacts. However, of these only Cl⋯H contacts occur at separations less than the sum of the van der Waals radii. The aforementioned π–π stacking inter­actions contribute 12.0% to the overall surface contacts. The calculation of the inter­action energies in the crystal indicates significant contributions from the dispersion term.

The crystal and mol­ecular structures of the title triorganotin di­thio­carbamate, [Sn(C6H5)3(C7H14NS2)], are described. The mol­ecular geometry about the metal atom is highly distorted being based on a C3S tetra­hedron as the di­thio­carbamate ligand is asymmetrically chelating to the tin centre. The close approach of the second thione-S atom [Sn⋯S = 2.9264 (4) Å] is largely responsible for the distortion. The mol­ecular packing is almost devoid of directional inter­actions with only weak phenyl-C—H⋯C(phen­yl) inter­actions, leading to centrosymmetric dimeric aggregates, being noted. An analysis of the calculated Hirshfeld surface points to the significance of H⋯H contacts, which contribute 66.6% of all contacts to the surface, with C⋯H/H⋯C [26.8%] and S⋯H/H⋯H [6.6%] contacts making up the balance.

In the title tri-substituted thio­urea derivative, C13H18N2O3S, the thione-S and carbonyl-O atoms lie, to a first approximation, to the same side of the mol­ecule [the S—C—N—C torsion angle is −49.3 (2)°]. The CN2S plane is almost planar (r.m.s. deviation = 0.018 Å) with the hy­droxy­ethyl groups lying to either side of this plane. One hy­droxy­ethyl group is orientated towards the thio­amide functionality enabling the formation of an intra­molecular N—H⋯O hydrogen bond leading to an S(7) loop. The dihedral angle [72.12 (9)°] between the planes through the CN2S atoms and the 4-tolyl ring indicates the mol­ecule is twisted. The experimental mol­ecular structure is close to the gas-phase, geometry-optimized structure calculated by DFT methods. In the mol­ecular packing, hydroxyl-O—H⋯O(hydrox­yl) and hydroxyl-O—H⋯S(thione) hydrogen bonds lead to the formation of a supra­molecular layer in the ab plane; no directional inter­actions are found between layers. The influence of the specified supra­molecular inter­actions is apparent in the calculated Hirshfeld surfaces and these are shown to be attractive in non-covalent inter­action plots; the inter­action energies point to the important stabilization provided by directional O—H⋯O hydrogen bonds.

In the title compound, bis­(2-meth­oxy­ethyl xanthato-κS)(N,N,N',N'-tetra­methyl­ethylenedi­amine-κ2N,N')zinc(II) acetone hemisolvate, [Zn(C4H7O2S2)2(C6H16N2)]·0.5C3H6O, the ZnII ion is coordinated by two N atoms of the N,N,N',N'-tetra­methyl­ethylenedi­amine ligand and two S atoms from two 2-meth­oxy­ethyl xanthate ligands. The amine ligand is disordered over two orientations and was modelled with refined occupancies of 0.538 (6) and 0.462 (6). The mol­ecular structure features two C—H⋯O and two C—H⋯S intra­molecular inter­actions. In the crystal, mol­ecules are linked by weak C—H⋯O and C—H⋯S hydrogen bonds, forming a three-dimensional supra­molecular architecture. The mol­ecular structure was optimized using density functional theory (DFT) at the B3LYP/6–311 G(d,p) level. The smallest HOMO–LUMO energy gap (3.19 eV) indicates the suitability of this crystal for optoelectronic applications. The mol­ecular electrostatic potential (MEP) further identifies the positive, negative and neutral electrostatic potential regions of the mol­ecules. Half a mol­ecule of disordered acetone was removed with the solvent-mask procedure in OLEX2 [Dolomanov et al. (2009). J. Appl. Cryst. 42, 339–341] and this contribition is included in the formula.

The title imidazo[1,2-a] pyridine derivative, C13H8Br2N2, was synthesized via a single-step reaction method. The title mol­ecule is planar, showing a dihedral angle of 0.62 (17)° between the phenyl and the imidazo[1,2-a] pyridine rings. An intra­molecular C—H⋯N hydrogen bond with an S(5) ring motif is present. In the crystal, a short H⋯H contact links adjacent mol­ecules into inversion-related dimers. The dimers are linked in turn by weak C—H⋯π and slipped π–π stacking inter­actions, forming layers parallel to (110). The layers are connected into a three-dimensional network by short Br⋯H contacts. Two-dimensional fingerprint plots and three-dimensional Hirshfeld surface analysis of the inter­molecular contacts reveal that the most important contributions for the crystal packing are from H⋯Br/Br⋯H (26.1%), H⋯H (21.7%), H⋯C/C⋯H (21.3%) and C⋯C (6.5%) inter­actions. Energy framework calculations suggest that the contacts formed between mol­ecules are largely dispersive in nature. Analysis of HOMO–LUMO energies from a DFT calculation reveals the pure π character of the aromatic rings with the highest electron density on the phenyl ring, and σ character of the electron density on the Br atoms. The HOMO–LUMO gap was found to be 4.343 eV.

In the title mol­ecule, C13H16N4O3, the mean planes of the phenyl and triazole rings are nearly perpendicular to one another as a result of the intra­molecular C—H⋯O and C—H⋯π(ring) inter­actions. In the crystal, layers parallel to (101) are generated by O—H⋯N, N—H⋯O and N—H⋯N hydrogen bonds. The layers are connected by inversion-related pairs of C—H⋯O hydrogen bonds. The experimental mol­ecular structure is close to the gas-phase geometry-optimized structure calculated by DFT methods. Hirshfeld surface analysis indicates that the most important inter­action involving hydrogen in the title compound is the H⋯H contact. The contribution of the H⋯O, H⋯N, and H⋯H contacts are 13.6, 16.1, and 54.6%, respectively.

The title compound, C15H22N4O5S, was prepared via alkyl­ation of 3-(chloro­meth­yl)-5-(pentan-3-yl)-1,2,4-oxa­diazole in anhydrous dioxane in the presence of tri­ethyl­amine. The thia­diazine ring has an envelope conformation with the S atom displaced by 0.4883 (6) Å from the mean plane through the other five atoms. The planar 1,2,4-oxa­diazole ring is inclined to the mean plane of the thia­diazine ring by 77.45 (11)°. In the crystal, mol­ecules are linked by C—H⋯N hydrogen bonds, forming chains propagating along the b-axis direction. Hirshfeld surface analysis and two-dimensional fingerprint plots have been used to analyse the inter­molecular contacts present in the crystal. Mol­ecular docking studies were use to evaluate the title compound as a potential system that inter­acts effectively with the capsid of the Hepatitis B virus (HBV), supported by an experimental in vitro HBV replication model.

The mol­ecular structure of the title bis-pyridyl substituted di­amide hydrate, C14H14N4O2·H2O, features a central C2N2O2 residue (r.m.s. deviation = 0.0205 Å) linked at each end to 3-pyridyl rings through methyl­ene groups. The pyridyl rings lie to the same side of the plane, i.e. have a syn-periplanar relationship, and form dihedral angles of 59.71 (6) and 68.42 (6)° with the central plane. An almost orthogonal relationship between the pyridyl rings is indicated by the dihedral angle between them [87.86 (5)°]. Owing to an anti disposition between the carbonyl-O atoms in the core, two intra­molecular amide-N—H⋯O(carbon­yl) hydrogen bonds are formed, each closing an S(5) loop. Supra­molecular tapes are formed in the crystal via amide-N—H⋯O(carbon­yl) hydrogen bonds and ten-membered {⋯HNC2O}2 synthons. Two symmetry-related tapes are linked by a helical chain of hydrogen-bonded water mol­ecules via water-O—H⋯N(pyrid­yl) hydrogen bonds. The resulting aggregate is parallel to the b-axis direction. Links between these, via methyl­ene-C—H⋯O(water) and methyl­ene-C—H⋯π(pyrid­yl) inter­actions, give rise to a layer parallel to (10overline{1}); the layers stack without directional inter­actions between them. The analysis of the Hirshfeld surfaces point to the importance of the specified hydrogen-bonding inter­actions, and to the significant influence of the water mol­ecule of crystallization upon the mol­ecular packing. The analysis also indicates the contribution of methyl­ene-C—H⋯O(carbon­yl) and pyridyl-C—H⋯C(carbon­yl) contacts to the stability of the inter-layer region. The calculated inter­action energies are consistent with importance of significant electrostatic attractions in the crystal.

The title homoleptic Schiff base complexes, [M(C14H9Cl2N2O)2], for M = CoII, (I), and CuII, (II), present distinct coordination geometries despite the Schiff base dianion coordinating via the phenolato-O and imine-N atoms in each case. For (I), the coordination geometry is based on a trigonal bipyramid whereas for (II), a square-planar geometry is found (Cu site symmetry overline{1}). In the crystal of (I), discernible supra­molecular layers in the ac plane are sustained by chloro­benzene-C—H⋯O(coordinated), chloro­benzene-C—H⋯π(fused-benzene ring) as well as π(fused-benzene, chloro­benzene)–π(chloro­benzene) inter­actions [inter-centroid separations = 3.6460 (17) and 3.6580 (16) Å, respectively]. The layers inter-digitate along the b-axis direction and are linked by di­chloro­benzene-C—H⋯π(fused-benzene ring) and π–π inter­actions between fused-benzene rings and between chloro­benzene rings [inter-centroid separations = 3.6916 (16) and 3.7968 (19) Å, respectively] . Flat, supra­molecular layers are also found in the crystal of (II), being stabilized by π–π inter­actions formed between fused-benzene rings and between chloro­benzene rings [inter-centroid separations = 3.8889 (15) and 3.8889 (15) Å, respectively]; these stack parallel to [10overline{1}] without directional inter­actions between them. The analysis of the respective calculated Hirshfeld surfaces indicate diminished roles for H⋯H contacts [26.2% (I) and 30.5% (II)] owing to significant contributions by Cl⋯H/H⋯Cl contacts [25.8% (I) and 24.9% (II)]. Minor contributions by Cl⋯Cl [2.2%] and Cu⋯Cl [1.9%] contacts are indicated in the crystals of (I) and (II), respectively. The inter­action energies largely arise from dispersion terms; the aforementioned Cu⋯Cl contact in (II) gives rise to the most stabilizing inter­action in the crystal of (II).

The crystal and mol­ecular structures of the title 1:2 co-crystal, C14H14N4O2·2C7H6O2, are described. The oxalamide mol­ecule has a (+)-anti­periplanar conformation with the 4-pyridyl residues lying to either side of the central, almost planar C2N2O2 chromophore (r.m.s. deviation = 0.0555 Å). The benzoic acid mol­ecules have equivalent, close to planar conformations [C6/CO2 dihedral angle = 6.33 (14) and 3.43 (10)°]. The formation of hy­droxy-O—H⋯N(pyrid­yl) hydrogen bonds between the benzoic acid mol­ecules and the pyridyl residues of the di­amide leads to a three-mol­ecule aggregate. Centrosymmetrically related aggregates assemble into a six-mol­ecule aggregate via amide-N—H⋯O(amide) hydrogen bonds through a 10-membered {⋯HNC2O}2 synthon. These are linked into a supra­molecular tape via amide-N—H⋯O(carbon­yl) hydrogen bonds and 22-membered {⋯HOCO⋯NC4NH}2 synthons. The contacts between tapes to consolidate the three-dimensional architecture are of the type methyl­ene-C—H⋯O(amide) and pyridyl-C—H⋯O(carbon­yl). These inter­actions are largely electrostatic in nature. Additional non-covalent contacts are identified from an analysis of the calculated Hirshfeld surfaces.

In the title compound, C12H15N3O5S, a tris­ubstituted thio­urea derivative, the central CN2S chromophore is almost planar (r.m.s. deviation = 0.018 Å) and the pendant hy­droxy­ethyl groups lie to either side of this plane. While to a first approximation the thione-S and carbonyl-O atoms lie to the same side of the mol­ecule, the S—C—N—C torsion angle of −47.8 (2)° indicates a considerable twist. As one of the hy­droxy­ethyl groups is orientated towards the thio­amide residue, an intra­molecular N—H⋯O hydrogen bond is formed which leads to an S(7) loop. A further twist in the mol­ecule is indicated by the dihedral angle of 65.87 (7)° between the planes through the CN2S chromophore and the 4-nitro­benzene ring. There is a close match between the experimental and gas-phase, geometry-optimized (DFT) mol­ecular structures. In the crystal, O—H⋯O and O—H⋯S hydrogen bonds give rise to supra­molecular layers propagating in the ab plane. The connections between layers to consolidate the three-dimensional architecture are of the type C—H⋯O, C—H⋯S and nitro-O⋯π. The nature of the supra­molecular association has been further analysed by a study of the calculated Hirshfeld surfaces, non-covalent inter­action plots and computational chemistry, all of which point to the significant influence and energy of stabilization provided by the conventional hydrogen bonds.

In the crystal structure of the title compound, C14H12ClNO, the mol­ecules are linked through C—H⋯O hydrogen bonds and C—H⋯π inter­actions, forming chains parallel to the [010] direction. π–π inter­actions and intra­molecular hydrogen bonds are also observed. The mol­ecular geometry of the title compound in the ground state has been calculated using density functional theory at the B3LYP level with the 6–311++G(2d,2p) basis set. Additionally, frontier mol­ecular orbital and mol­ecular electrostatic potential map analyses were performed.

The crystal and mol­ecular structures of the title organotin di­thio­carbamate compounds, [Sn(C6H5)3(C7H10NS2)] (I) and [Sn(C6H5)2(C7H10NS2)2] (II), present very distinct tin atom coordination geometries. In (I), the di­thio­carbamate ligand is asymmetrically coordinating with the resulting C3S2 donor set defining a coordination geometry inter­mediate between square-pyramidal and trigonal–bipyramidal. In (II), two independent mol­ecules comprise the asymmetric unit, which differ in the conformations of the allyl substituents and in the relative orientations of the tin-bound phenyl rings. The di­thio­carbamate ligands in (II) coordinate in an asymmetric mode but the Sn—S bonds are more symmetric than observed in (I). The resulting C2S4 donor set approximates an octa­hedral coordination geometry with a cis-disposition of the ipso-carbon atoms and with the more tightly bound sulfur atoms approximately trans. The only directional inter­molecular contacts in the crystals of (I) and (II) are of the type phenyl-C—H⋯π(phen­yl) and vinyl­idene-C—H⋯π(phen­yl), respectively, with each leading to a supra­molecular chain propagating along the a-axis direction. The calculated Hirshfeld surfaces emphasize the importance of H⋯H contacts in the crystal of (I), i.e. contributing 62.2% to the overall surface. The only other two significant contacts also involve hydrogen, i.e. C⋯H/H⋯C (28.4%) and S⋯H/H⋯S (8.6%). Similar observations pertain to the individual mol­ecules of (II), which are clearly distinguishable in their surface contacts, with H⋯H being clearly dominant (59.9 and 64.9%, respectively) along with C⋯H/H⋯C (24.3 and 20.1%) and S⋯H/H⋯S (14.4 and 13.6%) contacts. The calculations of energies of inter­action suggest dispersive forces make a significant contribution to the stabilization of the crystals. The exception is for the C—H⋯π contacts in (II) where, in addition to the dispersive contribution, significant contributions are made by the electrostatic forces.

The asymmetric unit of the title 1:2 co-crystal, C14H14N4O2·2C7H5ClO2, comprises two half mol­ecules of oxalamide (4LH2), as each is disposed about a centre of inversion, and two mol­ecules of 4-chloro­benzoic acid (CBA), each in general positions. Each 4LH2 mol­ecule has a (+)anti­periplanar conformation with the pyridin-4-yl residues lying to either side of the central, planar C2N2O2 chromophore with the dihedral angles between the respective central core and the pyridyl rings being 68.65 (3) and 86.25 (3)°, respectively, representing the major difference between the independent 4LH2 mol­ecules. The anti conformation of the carbonyl groups enables the formation of intra­molecular amide-N—H⋯O(amide) hydrogen bonds, each completing an S(5) loop. The two independent CBA mol­ecules are similar and exhibit C6/CO2 dihedral angles of 8.06 (10) and 17.24 (8)°, indicating twisted conformations. In the crystal, two independent, three-mol­ecule aggregates are formed via carb­oxy­lic acid-O—H⋯N(pyrid­yl) hydrogen bonding. These are connected into a supra­molecular tape propagating parallel to [100] through amide-N—H⋯O(amide) hydrogen bonding between the independent aggregates and ten-membered {⋯HNC2O}2 synthons. The tapes assemble into a three-dimensional architecture through pyridyl- and methyl­ene-C—H⋯O(carbon­yl) and CBA-C—H⋯O(amide) inter­actions. As revealed by a more detailed analysis of the mol­ecular packing by calculating the Hirshfeld surfaces and computational chemistry, are the presence of attractive and dispersive Cl⋯C=O inter­actions which provide inter­action energies approximately one-quarter of those provided by the amide-N—H⋯O(amide) hydrogen bonding sustaining the supra­molecular tape.

In the title compound, C9H10ClNOS, the amide functional group –C(=O)NH– adopts a trans conformation with the four atoms nearly coplanar. This conformation promotes the formation of a C(4) hydrogen-bonded chain propagating along the [010] direction. The central part of the mol­ecule, including the six-membered ring, the S and N atoms, is fairly planar (r.m.s. deviation of 0.014). The terminal methyl group and the C(=O)CH2 group are slightly deviating out-of-plane while the terminal Cl atom is almost in-plane. Hirshfeld surface analysis of the title compound suggests that the most significant contacts in the crystal are H⋯H, H⋯Cl/Cl⋯H, H⋯C/C⋯H, H⋯O/O⋯H and H⋯S/S⋯H. π–π inter­actions between inversion-related mol­ecules also contribute to the crystal packing. DFT calculations have been performed to optimize the structure of the title compound using the CAM-B3LYP functional and the 6–311 G(d,p) basis set. The theoretical absorption spectrum of the title compound was calculated using the TD–DFT method. The analysis of frontier orbitals revealed that the π–π* electronic transition was the major contributor to the absorption peak in the electronic spectrum.

The X-ray crystal structure of the title phthalazin-1-one derivative, C17H16N2O3S {systematic name: 2-[(2,4,6-tri­methyl­benzene)­sulfon­yl]-1,2-di­hydro­phthalazin-1-one}, features a tetra­hedral sulfoxide-S atom, connected to phthalazin-1-one and mesityl residues. The dihedral angle [83.26 (4)°] between the organic substituents is consistent with the mol­ecule having the shape of the letter V. In the crystal, phthalazinone-C6-C—H⋯O(sulfoxide) and π(phthalazinone-N2C4)–π(phthalazinone-C6) stacking [inter-centroid distance = 3.5474 (9) Å] contacts lead to a linear supra­molecular tape along the a-axis direction; tapes assemble without directional inter­actions between them. The analysis of the calculated Hirshfeld surfaces confirm the importance of the C—H⋯O and π-stacking inter­actions but, also H⋯H and C—H⋯C contacts. The calculation of the inter­action energies indicate the importance of dispersion terms with the greatest energies calculated for the C—H⋯O and π-stacking inter­actions.

The present work reports on the charge and spin density modelling of YTiO3 in its ferromagnetic state (TC = 27 K). Accurate polarized neutron diffraction and high-resolution X-ray diffraction (XRD) experiments were carried out on a single crystal at the ORPHÉE reactor (LLB) and SPRING8 synchrotron source. The experimental data are modelled by the spin resolved pseudo-atomic multipolar model (Deutsch et al., 2012). The refinement strategy is discussed and the result of this electron density modelling is compared with that from XRD measured at 100 K and with density functional theory calculations. The results show that the spin and charge densities around the Ti atom have lobes directed away from the O atoms, confirming the filling of the t2g orbitals of the Ti atom. The dxy orbital is less populated than dxz and dyz, which is a sign of a partial lift of degeneracy of the t2g orbitals. This study confirms the orbital ordering at low temperature (20 K), which is already present in the paramagnetic state above the ferromagnetic transition (100 K).

Radiation damage is the most fundamental limitation for achieving high resolution in electron cryo-microscopy (cryo-EM) of biological samples. The effects of radiation damage are reduced by liquid-helium cooling, although the use of liquid helium is more challenging than that of liquid nitrogen. To date, the benefits of liquid-nitrogen and liquid-helium cooling for single-particle cryo-EM have not been compared quantitatively. With recent technical and computational advances in cryo-EM image recording and processing, such a comparison now seems timely. This study aims to evaluate the relative merits of liquid-helium cooling in present-day single-particle analysis, taking advantage of direct electron detectors. Two data sets for recombinant mouse heavy-chain apoferritin cooled with liquid-nitrogen or liquid-helium to 85 or 17 K were collected, processed and compared. No improvement in terms of resolution or Coulomb potential map quality was found for liquid-helium cooling. Interestingly, beam-induced motion was found to be significantly higher with liquid-helium cooling, especially within the most valuable first few frames of an exposure, thus counteracting any potential benefit of better cryoprotection that liquid-helium cooling may offer for single-particle cryo-EM.

The application of thermoelectrics for energy harvesting depends strongly on operational reliability and it is therefore desirable to investigate the structural integrity of materials under operating conditions. We have developed an operando setup capable of simultaneously measuring X-ray scattering data and electrical resistance on pellets subjected to electrical current. Here, operando investigations of β-Zn4Sb3 are reported at current densities of 0.5, 1.14 and 2.3 A mm−2. At 0.5 A mm−2 no sample decomposition is observed, but Rietveld refinements reveal increased zinc occupancy from the anode to the cathode demonstrating zinc migration under applied current. At 1.14 A mm−2 β-Zn4Sb3 decomposes into ZnSb, but pair distribution function analysis shows that Zn2Sb2 units are preserved during the decomposition. This identifies the mobile zinc in β-Zn4Sb3 as the linkers between the Zn2Sb2 units. At 2.3 A mm−2 severe Joule heating triggers transition into the γ-Zn4Sb3 phase, which eventually decomposes into ZnSb, demonstrating Zn ion mobility also in γ-Zn4Sb3 under electrical current.

Human muscarinic receptor M4 belongs to the class A subfamily of the G-protein-coupled receptors (GPCRs). M4 has emerged as an attractive drug target for the treatment of Alzheimer's disease and schizophrenia. Recent results showed that M4-mediated cholinergic transmission is related to motor symptoms in Parkinson's disease. Selective ligand design for the five muscarinic acetylcholine receptor (mAchR) subtypes currently remains challenging owing to the high sequence and structural similarity of their orthosteric binding pockets. In order to obtain M4-selective antagonists, a new approach was tried to lock M4 into an inactive form by rationally designing an N4497.49R mutation, which mimics the allosteric sodium binding in the conserved sodium site usually found in class A GPCRs. In addition, the crystal structure of the mutation-induced inactive M4 was determined. By comparative analysis with other mAchR structures, followed by functional assays, the N4497.49R mutation was shown to stabilize M4 into an inactive state. Virtual screening of a focused ligand library using the crystal structure showed that the inactive M4 prefers antagonists much more than agonists. This study provides a powerful mutation strategy to stabilize GPCRs in inactive states and facilitate their structure determination.

X-ray diffraction studies of crystals under pressure and quantitative experimental charge density analysis are among the most demanding types of crystallographic research. A successful feasibility study of the electron density in the mineral grossular under 1 GPa pressure conducted at the CRISTAL beamline at the SOLEIL synchrotron is presented in this work. A single crystal was placed in a diamond anvil cell, but owing to its special design (wide opening angle), short synchrotron wavelength and the high symmetry of the crystal, data with high completeness and high resolution were collected. This allowed refinement of a full multipole model of experimental electron distribution. Results are consistent with the benchmark measurement conducted without a diamond-anvil cell and also with the literature describing investigations of similar structures. Results of theoretical calculations of electron density distribution on the basis of dynamic structure factors mimic experimental findings very well. Such studies allow for laboratory simulations of processes which take place in the Earth's mantle.

TatD has been thoroughly investigated as a DNA-repair enzyme and an apoptotic nuclease, and still-unknown TatD-related DNases are considered to play crucial cellular roles. However, studies of TatD from Gram-positive bacteria have been hindered by an absence of atomic detail and the resulting inability to determine function from structure. In this study, an X-ray crystal structure of SAV0491, which is the TatD enzyme from the Gram-positive bacterium Staphylococcus aureus (SaTatD), is reported at a high resolution of 1.85 Å with a detailed atomic description. Although SaTatD has the common TIM-barrel fold shared by most TatD-related homologs, and PDB entry 2gzx shares 100% sequence identity with SAV0491, the crystal structure of SaTatD revealed a unique binding mode of two phosphates interacting with two Ni2+ ions. Through a functional study, it was verified that SaTatD has Mg2+-dependent nuclease activity as a DNase and an RNase. In addition, structural comparison with TatD homologs and the identification of key residues contributing to the binding mode of Ni2+ ions and phosphates allowed mutational studies to be performed that revealed the catalytic mechanism of SaTatD. Among the key residues composing the active site, the acidic residues Glu92 and Glu202 had a critical impact on catalysis by SaTatD. Furthermore, based on the binding mode of the two phosphates and structural insights, a putative DNA-binding mode of SaTatD was proposed using in silico docking. Overall, these findings may serve as a good basis for understanding the relationship between the structure and function of TatD proteins from Gram-positive bacteria and may provide critical insights into the DNA-binding mode of SaTatD.

Many biologists are now routinely seeking to determine the three-dimensional structures of their proteins of choice, illustrating the importance of this knowledge, but also of the simplification and streamlining of structure-determination processes. Despite the fact that most software packages offer simple pipelines, for the non-expert navigating the outputs and understanding the key aspects can be daunting. Here, the structure determination of the type IV pili (TFP) protein PilA1 from Clostridioides difficile is used to illustrate the different steps involved, the key decision criteria and important considerations when using the most common pipelines and software. Molecular-replacement pipelines within CCP4i2 are presented to illustrate the more commonly used processes. Previous knowledge of the biology and structure of TFP pilins, particularly the presence of a long, N-terminal α-helix required for pilus formation, allowed informed decisions to be made during the structure-determination strategy. The PilA1 structure was finally successfully determined using ARCIMBOLDO and the ab initio MR strategy used is described.

This paper discusses the full structural solution of the hybrid perovskite formamidinium lead tribromide (FAPbBr3) and its temperature-dependent phase transitions in the range from 3 K to 300 K using neutron powder diffraction and synchrotron X-ray diffraction. Special emphasis is put on the influence of deuteration on formamidinium, its position in the unit cell and disordering in comparison to fully hydrogenated FAPbBr3. The temperature-dependent measurements show that deuteration critically influences the crystal structures, i.e. results in partially-ordered temperature-dependent structural modifications in which two symmetry-independent molecule positions with additional dislocation of the molecular centre atom and molecular angle inclinations are present.

Small-angle scattering tensor tomography (SASTT) is a recently developed technique able to tomographically reconstruct the 3D reciprocal space from voxels within a bulk volume. SASTT extends the concept of X-ray computed tomography, which typically reconstructs scalar values, by reconstructing a tensor per voxel, which represents the local nanostructure 3D organization. In this study, the nanostructure orientation in a human trabecular-bone sample obtained by SASTT was validated by sectioning the sample and using 3D scanning small-angle X-ray scattering (3D sSAXS) to measure and analyze the orientation from single voxels within each thin section. Besides the presence of cutting artefacts from the slicing process, the nanostructure orientations obtained with the two independent methods were in good agreement, as quantified with the absolute value of the dot product calculated between the nanostructure main orientations obtained in each voxel. The average dot product per voxel over the full sample containing over 10 000 voxels was 0.84, and in six slices, in which fewer cutting artefacts were observed, the dot product increased to 0.91. In addition, SAXS tensor tomography not only yields orientation information but can also reconstruct the full 3D reciprocal-space map. It is shown that the measured anisotropic scattering for individual voxels was reproduced from the SASTT reconstruction in each voxel of the 3D sample. The scattering curves along different 3D directions are validated with data from single voxels, demonstrating SASTT's potential for a separate analysis of nanostructure orientation and structural information from the angle-dependent intensity distribution.

This study relates to the INFN project SYRMA-3D for in vivo phase-contrast breast computed tomography using the SYRMEP synchrotron radiation beamline at the ELETTRA facility in Trieste, Italy. This peculiar imaging technique uses a novel dosimetric approach with respect to the standard clinical procedure. In this study, optimization of the acquisition procedure was evaluated in terms of dose delivered to the breast. An offline dose monitoring method was also investigated using radiochromic film dosimetry. Various irradiation geometries have been investigated for scanning the prone patient's pendant breast, simulated by a 14 cm-diameter polymethylmethacrylate cylindrical phantom containing pieces of calibrated radiochromic film type XR-QA2. Films were inserted mid-plane in the phantom, as well as wrapped around its external surface, and irradiated at 38 keV, with an air kerma value that would produce an estimated mean glandular dose of 5 mGy for a 14 cm-diameter 50% glandular breast. Axial scans were performed over a full rotation or over 180°. The results point out that a scheme adopting a stepped rotation irradiation represents the best geometry to optimize the dose distribution to the breast. The feasibility of using a piece of calibrated radiochromic film wrapped around a suitable holder around the breast to monitor the scan dose offline is demonstrated.

A Thomson scattering X-ray source can provide quasi-monochromatic, continuously energy-tunable, polarization-controllable and high-brightness X-rays, which makes it an excellent tool for X-ray fluorescence computed tomography (XFCT). In this paper, we examined the suppression of Compton scattering background in XFCT using the linearly polarized X-rays and the implementation feasibility of linearly polarized XFCT based on this type of light source, concerning the influence of phantom attenuation and the sampling strategy, its advantage over K-edge subtraction computed tomography (CT), the imaging time, and the potential pulse pile-up effect by Monte Carlo simulations. A fan beam and pinhole collimator geometry were adopted in the simulation and the phantom was a polymethyl methacrylate cylinder inside which were gadolinium (Gd)-loaded water solutions with Gd concentrations ranging from 0.2 to 4.0 wt%. Compared with the case of vertical polarization, Compton scattering was suppressed by about 1.6 times using horizontal polarization. An accurate image of the Gd-containing phantom was successfully reconstructed with both spatial and quantitative identification, and good linearity between the reconstructed value and the Gd concentration was verified. When the attenuation effect cannot be neglected, one full cycle (360°) sampling and the attenuation correction became necessary. Compared with the results of K-edge subtraction CT, the contrast-to-noise ratio values of XFCT were improved by 2.03 and 1.04 times at low Gd concentrations of 0.2 and 0.5 wt%, respectively. When the flux of a Thomson scattering light source reaches 1013 photons s−1, it is possible to finish the data acquisition of XFCT at the minute or second level without introducing pulse pile-up effects.

The laser annealing process for AuNi nanoparticles has been visualized using coherent X-ray diffraction imaging (CXDI). AuNi bimetallic alloy nanoparticles, originally phase separated due to the miscibility gap, transform to metastable mixed alloy particles with rounded surface as they are irradiated by laser pulses. A three-dimensional CXDI shows that the internal part of the AuNi particles is in the mixed phase with preferred compositions at ∼29 at% of Au and ∼90 at% of Au.

The composition of occupied and unoccupied electronic states in the vicinity of Fermi energies is vital for all materials and relates to their physical, chemical and mechanical properties. This work demonstrates how the combination of resonant and non-resonant X-ray emission spectroscopies supplemented with theoretical modelling allows for quantitative analysis of electronic states in 5d transition metal and metal-oxide materials. Application of X-rays provides element selectivity that, in combination with the penetrating properties of hard X-rays, allows determination of the composition of electronic states under working conditions, i.e. non-vacuum environment. Tungsten metal and tungsten oxide are evaluated to show the capability to simultaneously assess composition of around-band-gap electronic states as well as the character and magnitude of the crystal field splitting.

Strain tensor measurements are important for understanding elastic and plastic deformation, but full bulk strain tensor measurement techniques are still lacking, in particular for dynamic loading. Here, such a methodology is reported, combining imaging-based strain field mapping and simultaneous X-ray diffraction for four typical loading modes: one-dimensional strain/stress compression/tension. Strain field mapping resolves two in-plane principal strains, and X-ray diffraction analysis yields volumetric strain, and thus the out-of-plane principal strain. This methodology is validated against direct molecular dynamics simulations on nanocrystalline tantalum. This methodology can be implemented with simultaneous X-ray diffraction and digital image correlation in synchrotron radiation or free-electron laser experiments.

Nanoporous anodic aluminium oxide (AAO) membranes are promising host systems for confinement of condensed matter. Characterizing their structure and composition is thus of primary importance for studying the behavior of confined objects. Here a novel methodology to extract quantitative information on the structure and composition of well defined AAO membranes by combining small-angle neutron scattering (SANS) measurements and scanning electron microscopy (SEM) imaging is reported. In particular, (i) information about the pore hexagonal arrangement is extracted from SEM analysis, (ii) the best SANS experimental conditions to perform reliable measurements are determined and (iii) a detailed fitting method is proposed, in which the probed length in the fitting model is a critical parameter related to the longitudinal pore ordering. Finally, to validate this strategy, it is applied to characterize AAOs prepared under different conditions and it is shown that the experimental SANS data can be fully reproduced by a core/shell model, indicating the existence of a contaminated shell. This original approach, based on a detailed and complete description of the SANS data, can be applied to a variety of confining media and will allow the further investigation of condensed matter under confinement.

The distribution of plastic relaxation defects is studied using a nondestructive sub-micrometre X-ray diffraction scanning technique.

Very asymmetric crystal diffraction was obtained from a finely polished silicon crystal set to reflect in Bragg diffraction at grazing incidence for the (333) reflection. The angle of incidence to achieve Bragg diffraction was varied between 1.08° and 0.33° by changing the X-ray energy from 8.100 to 8.200 keV. Topographic images obtained as the crystal was rocked were used to identify the effects of surface undulations, and the results are compared with dynamical X-ray diffraction calculations made with the Takagi–Taupin equations specialized to a surface having convex or concave features, as reported in an accompanying paper.

A detailed theoretical and experimental comparison of dark-field electron holography (DFEH) and high-resolution X-ray diffraction (HRXRD) is performed. Both techniques are being applied to measure elastic strain in an array of transistors and the role of the geometric phase is emphasized.

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 […]

The post Study aims to give endangered Shenandoah salamander better odds at survival appeared first on Smithsonian Insider.

A recent survey of the bottom-dwelling animals of the Chesapeake has revealed that communities of even these relatively hardy organisms are under stress. Many regions of the bay are becoming inhospitable to bottom-dwelling animals because of a lack of oxygen—a condition known as “hypoxia.”

The post Bottom-dwelling creatures in the Chesapeake Bay need more oxygen, study finds. appeared first on Smithsonian Insider.

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.

The post A dry spring in Panama means more sulfur butterflies, study reveals appeared first on Smithsonian Insider.

Invasive species, contaminants, excessive nutrient's and sediment are just some of the many factors threatening sensitive wetlands and seagrass beds.

The post Smithsonian to lead study on degradation of nearshore coastal habitats of the Chesapeake appeared first on Smithsonian Insider.