‘State government has failed to protect the people of Delhi from the virus’

Hyderabad International Airport facilitated the first arrival evacuation flight from Kuwait on Saturday.This is the first flight to Hyderabad and is p

A total of 15,25,631 tests have been conducted so far across 332 government and 121 private laboratories.

A fabrication method comprising near-field holography (NFH) with an electron beam lithography (EBL)-written phase mask was developed to fabricate soft X-ray varied-line-spacing gratings (VLSGs). An EBL-written phase mask with an area of 52 mm × 30 mm and a central line density greater than 3000 lines mm−1 was used. The introduction of the EBL-written phase mask substantially simplified the NFH optics for pattern transfer. The characterization of the groove density distribution and diffraction efficiency of the fabricated VLSGs indicates that the EBL–NFH method is feasible and promising for achieving high-accuracy groove density distributions with corresponding image properties. Vertical stray light is suppressed in the soft X-ray spectral range.

A method is presented for the automatic building of nucleotide chains into electron density which is fast enough to be used in interactive model-building software. Likely nucleotides lying in the vicinity of the current view are located and then grown into connected chains in a fraction of a second. When this development is combined with existing tools, assisted manual model building is as simple as or simpler than for proteins.

Tuning in to a Glacial Symphony  Eos

The enzyme 4-hydroxy-tetrahydrodipicolinate synthase (DapA) is involved in the production of lysine and precursor molecules for peptidoglycan synthesis. In a multistep reaction, DapA converts pyruvate and l-aspartate-4-semialdehyde to 4-hydroxy-2,3,4,5-tetrahydrodipicolinic acid. In many organisms, lysine binds allosterically to DapA, causing negative feedback, thus making the enzyme an important regulatory component of the pathway. Here, the 2.1 Å resolution crystal structure of DapA from the thermoacidophilic methanotroph Methylacidiphilum fumariolicum SolV is reported. The enzyme crystallized as a contaminant of a protein preparation from native biomass. Genome analysis reveals that M. fumariolicum SolV utilizes the recently discovered aminotransferase pathway for lysine biosynthesis. Phylogenetic analyses of the genes involved in this pathway shed new light on the distribution of this pathway across the three domains of life.

The setup and operation of an industrial cryo-EM laboratory is described.

In the title 1:1 co-crystal [systematic name: 6-chloro­pyridin-2-amine–penta­nedioic acid (1/1)], C5H5ClN2·C5H8O4, the pyridine ring is essentially planar, with a maximum deviation of 0.003 (1) Å. The base and acid mol­ecules are linked via N—H⋯O and O—H⋯N hydrogen bonds, while inversion-related acid mol­ecules are linked via pairs of O—H⋯O hydrogen bonds. These inter­actions together with a C—H⋯O hydrogen bond connect the two components, forming (001) sheets.

6-Methyluracil, C5H6N2O2, exists in two crystalline phases: form (I), monoclinic, space group P21/c [Reck et al. (1988). Acta Cryst. A44, 417–421] and form (II), monoclinic, space group C2/c [Leonidov et al. (1993). Russ. J. Phys. Chem. 67, 2220–2223]. The structure of polymorph (II) has been redetermined providing a significant increase in the precision of the derived geometric parameters. In the crystal, mol­ecules form ribbons approximately running parallel to the c-axis direction through N—H⋯O hydrogen bonds. The radical differences observed between the crystal packing of the two polymorphs may be responsible in form (II) for an increase in the contribution of the polar canonical forms C—(O−)=N—H+ relative to the neutral canonical form C(=O)—N—H induced by hydrogen-bonding inter­actions.

The title mol­ecule, C11H8F3NO3, adopts a cis configuration across the –C=C– double bond in the side chain and the dihedral angle between the phenyl ring and side chain is 47.35 (1)°. The –COOH group adopts a syn conformation (O=C—O—H = 0°), unlike the anti conformation observed in related maleamic acids. In the crystal, inversion dimers linked by pairs of O—H⋯O hydrogen bonds are connected via N—H⋯O hydrogen bonds and C—H⋯O inter­actions into (100) sheets, which are cross-linked by another C—H⋯O inter­action to result in a three-dimensional network. The Hirshfeld surface fingerprint plots show that the highest contribution to surface contacts arises from O⋯H/H⋯O contacts (26.5%) followed by H⋯F/F⋯H (23.4%) and H⋯H (17.3%).

The structure of zymonic acid (systematic name: 4-hy­droxy-2-methyl-5-oxo-2,5-di­hydro­furan-2-carb­oxy­lic acid), C6H6O5, which had previously eluded crystallographic determination, is presented here for the first time. It forms by intra­molecular condensation of parapyruvic acid, which is the product of aldol condensation of pyruvic acid. A redetermination of the crystal structure of pyruvic acid (systematic name: 2-oxo­propanoic acid), C3H4O3, at low temperature (90 K) and with increased precision, is also presented [for the previous structure, see: Harata et al. (1977). Acta Cryst. B33, 210–212]. In zymonic acid, the hy­droxy­lactone ring is close to planar (r.m.s. deviation = 0.0108 Å) and the dihedral angle between the ring and the plane formed by the bonds of the methyl and carb­oxy­lic acid carbon atoms to the ring is 88.68 (7)°. The torsion angle of the carb­oxy­lic acid group relative to the ring is 12.04 (16)°. The pyruvic acid mol­ecule is almost planar, having a dihedral angle between the carb­oxy­lic acid and methyl-ketone groups of 3.95 (6)°. Inter­molecular inter­actions in both crystal structures are dominated by hydrogen bonding. The common R22(8) hydrogen-bonding motif links carb­oxy­lic acid groups on adjacent mol­ecules in both structures. In zymonic acid, this results in dimers about a crystallographic twofold of space group C2/c, which forces the carb­oxy­lic acid group to be disordered exactly 50:50, which scrambles the carbonyl and hydroxyl groups and gives an apparent equalization of the C—O bond lengths [1.2568 (16) and 1.2602 (16) Å]. The other hydrogen bonds in zymonic acid (O—H⋯O and weak C—H⋯O), link mol­ecules across a 21-screw axis, and generate an R22(9) motif. These hydrogen-bonding inter­actions propagate to form extended pleated sheets in the ab plane. Stacking of these zigzag sheets along c involves only van der Waals contacts. In pyruvic acid, inversion-related mol­ecules are linked into R22(8) dimers, with van der Waals inter­actions between dimers as the only other inter­molecular contacts.

The title compound, C11H8O5·(CH3)2SO, is a new coumarin derivative. The asymmetric unit contains two coumarin mol­ecules (A and B) and two di­methyl­sulfoxide solvent mol­ecules (A and B). The dihedral angle between the pyran and benzene rings in the chromene moiety is 3.56 (2)° for mol­ecule A and 1.83 (2)° for mol­ecule B. In mol­ecule A, the dimethyl sulfoxide sulfur atom is disordered over two positions with a refined occupancy ratio of 0.782 (5):0.218 (5). In the crystal, mol­ecules are linked by O—H⋯O hydrogen bonds, forming chains running along the c-axis direction. The chains are linked by C—H⋯O hydrogen bonds, forming layers parallel to the ac plane. In addition, there are also C—H⋯π and π–π inter­actions present within the layers. The inter­molecular contacts in the crystal have been analysed using Hirshfeld surface analysis and two-dimensional fingerprint plots, which indicate that the most important contributions to the packing are from H⋯H (33.9%) and O⋯H/H⋯O (41.2%) contacts.

The title compound, C8H4Br2O4·C2H6O2, crystallizes with one-half of a 2,5-di­bromo­terephthalic acid (H2Br2tp) mol­ecule and one-half of an ethyl­ene glycol (EG) mol­ecule in the the asymmetric unit. The whole mol­ecules are generated by application of inversion symmetry. The H2Br2tp mol­ecule is not planar, with the di­bromo­benzene ring system inclined by a dihedral angle of 18.62 (3)° to the carb­oxy­lic group. In the crystal, the H2Br2tp and EG mol­ecules are linked into sheets propagating parallel to (overline{1}01) through O—H⋯O hydrogen bonds, thereby forming R44 (12) and R44 (28) graph-set motifs. Br⋯O and weak π–π stacking inter­actions are also observed. Hirshfeld surface analysis was used to confirm the existence of these inter­actions.

Two compounds, 1,3-diethyl-5-{(2E,4E)-6-[(E)-1,3,3-tri­methyl­indolin-2-yl­idene]hexa-2,4-dien-1-yl­idene}pyrimidine-2,4,6(1H,3H,5H)-trione or TMI, C25H29N3O3, and 1,3-diethyl-2-sulfanyl­idene-5-[2-(1,3,3-tri­methyl­indolin-2-yl­idene)ethyl­idene]di­hydro­pyrimidine-4,6(1H,5H)-dione or DTB, C21H25N3O2S, have been crystallized and studied. These compounds contain the same indole derivative donor group and differ in their acceptor groups (in TMI it contains oxygen in the para position, and in DTB sulfur) and the length of the π-bridge. In both materials, mol­ecules are packed in a herringbone manner with differences in the twist and fold angles. In both structures, the mol­ecules are connected by weak C—H⋯O and/or C—H⋯S bonds.

The structures of three compounds of 3-chloro-2-nitro­benzoic acid with 5-nitro­quinoline, (I), 6-nitro­quinoline, (II), and 8-hy­droxy­quinoline, (III), have been determined at 190 K. In each of the two isomeric compounds, (I) and (II), C7H4ClNO4·C9H6N2O2, the acid and base mol­ecules are held together by O—H⋯N and C—H⋯O hydrogen bonds. In compound (III), C9H8NO+·C7H3ClNO4−, an acid–base inter­action involving H-atom transfer occurs and the H atom is located at the N site of the base mol­ecule. In the crystal of (I), the hydrogen-bonded acid–base units are linked by C—H⋯O hydrogen bonds, forming a tape structure along the b-axis direction. Adjacent tapes, which are related by a twofold rotation axis, are linked by a third C—H⋯O hydrogen bond, forming wide ribbons parallel to the (overline{1}03) plane. These ribbons are stacked via π–π inter­actions between the quinoline ring systems [centroid–centroid distances = 3.4935 (5)–3.7721 (6) Å], forming layers parallel to the ab plane. In the crystal of (II), the hydrogen-bonded acid–base units are also linked into a tape structure along the b-axis direction via C—H⋯O hydrogen bonds. Inversion-related tapes are linked by further C—H⋯O hydrogen bonds to form wide ribbons parallel to the (overline{3}08) plane. The ribbons are linked by weak π–π inter­actions [centroid–centroid distances = 3.8016 (8)–3.9247 (9) Å], forming a three-dimensional structure. In the crystal of (III), the cations and the anions are alternately linked via N—H⋯O and O—H⋯O hydrogen bonds, forming a 21 helix running along the b-axis direction. The cations and the anions are further stacked alternately in columns along the a-axis direction via π–π inter­actions [centroid–centroid distances = 3.8016 (8)–3.9247 (9) Å], and the mol­ecular chains are linked into layers parallel to the ab plane through these inter­actions.

In the title 1:1 cocrystal, C7H4ClNO4·C6H6N2O, nicotinamide (NIC) and 2-chloro-5-nitro­benzoic acid (CNBA) cocrystallize with one mol­ecule each of NIC and CNBA in the asymmetric unit. In this structure, CNBA and NIC form hydrogen bonds through O—H⋯N, N—H⋯O and C—H⋯O inter­actions along with N—H⋯O dimer hydrogen bonds of NIC. Further additional weak π–π inter­actions stabilize the mol­ecular assembly of this cocrystal.

The structures of two isomeric com­pounds of 5-nitro­quinoline with chloro- and nitro-substituted benzoic acid, namely, 2-chloro-4-nitro­benzoic acid–5-nitro­quinoline (1/1), (I), and 5-chloro-2-nitro­benzoic acid–5-nitro­quinoline (1/1), (II), both C7H4ClNO4·C9H6N2O2, have been determined at 190 K. In each com­pound, the acid and base mol­ecules are held together by an O—H⋯N hydrogen bond. In the crystal of (I), the hydrogen-bonded acid–base units are linked by a C—H⋯O hydrogen bond, forming a tape structure along [1overline{2}0]. The tapes are stacked into a layer parallel to the ab plane via N—O⋯π inter­actions between the nitro group of the base mol­ecule and the quinoline ring system. The layers are further linked by other C—H⋯O hydrogen bonds, forming a three-dimensional network. In the crystal of (II), the hydrogen-bonded acid–base units are linked into a wide ribbon structure running along [1overline{1}0] via C—H⋯O hydrogen bonds. The ribbons are further linked via another C—H⋯O hydrogen bond, forming a layer parallel to (110). Weak π–π inter­actions [centroid–centroid distances of 3.7080 (10) and 3.7543 (9) Å] are observed between the quinoline ring systems of adjacent layers. Hirshfeld surfaces for the 5-nitro­quinoline mol­ecules of the two com­pounds mapped over shape index and dnorm were generated to visualize the weak inter­molecular inter­actions.

A zinc metal–organic framework, namely poly[bis­(N,N-di­ethyl­formamide)(μ4-naphthalene-2,6-di­carboxyl­ato)(μ2-naphthalene-2,6-di­carboxyl­ato)dizinc(II)], [Zn(C12H6O4)(C15H11NO)]n, built from windmill-type secondary building units and forming zigzag shaped two-dimensional stacked layers, has been solvothermally synthesized from naphthalene-2,6-di­carb­oxy­lic acid and zinc(II) acetate as the metal source in N,N-di­ethyl­formamide containing small amounts of formic acid.

Highly Brønsted-acidic boron trifluoride monohydrate, a widely used `super acid-catalyst', is a colourless fuming liquid that releases BF3 at room temperature. Com­pared to the liquid com­ponents, i.e. boron trifluoride monohydrate and 1,4-dioxane, their 1:1 adduct, BF3H2O·C4H8O2, is a solid with pronounced thermal stability (m.p. 401–403 K). The crystal structure of the long-time-stable easy-to-handle and weighable com­pound is reported along with new preparative aspects and the results of 1H, 11B, 13C and 19F spectroscopic investigations, particularly documenting its high Brønsted acidity in aceto­nitrile solution. The remarkable stability of solid BF3H2O·C4H8O2 is attributed to the chain structure established by O—H⋯O hydrogen bonds of exceptional strength {O2⋯H1—O1 [O⋯O = 2.534 (3) Å] and O1—H1⋯O3i [2.539 (3) Å] in the concatenating unit >O2⋯H1—O1—H2⋯O3i<}, taking into account the mol­ecular (non-ionic) character of the structural moieties. Indirectly, this structural feature documents the outstanding acidification of the H2O mol­ecule bound to BF3 and reflects the super acid nature of BF3H2O. In detail, the C22(7) zigzag chain system of hydrogen bonding in the title structure is characterized by the double hydrogen-bond donor and double (κO,κO') hydrogen-bond acceptor functionality of the aqua ligand and dioxane molecule, respectively, the almost equal strength of both hydrogen bonds, the approximatety linear arrangement of the dioxane O atoms and the two neighbouring water O atoms. Furthermore, the approximately planar arrangement of B, F and O atoms in sheets perpendicular to the c axis of the ortho­rhom­bic unit cell is a characteristic structural feature.

A reaction of copper(II) carbonate and potassium 4-sulfo­benzoic acid in water acidified with hydro­chloric acid yielded two crystalline products. Tetra­aqua­bis­(4-carb­oxy­benzene­sulfonato)­copper(II) dihydrate, [Cu(O3SC6H4CO2H)2(H2O)4]·2H2O, (I), crystallizes in the triclinic space group Poverline{1} with the Cu2+ ions located on centers of inversion. Each copper ion is coordinated to four water mol­ecules in a square plane with two sulfonate O atoms in the apical positions of a Jahn–Teller-distorted octa­hedron. The carboxyl­ate group is protonated and not involved in coordination to the metal ions. The complexes pack so as to create a layered structure with alternating inorganic and organic domains. The packing is reinforced by several O—H⋯O hydrogen bonds involving coordinated and non-coordinated water mol­ecules, the carb­oxy­lic acid group and the sulfonate group. Hexa­aqua­copper(II) 4-carb­oxy­benzene­sulfonate, [Cu(H2O)6](O3SC6H4CO2H)2, (II), also crystallizes in the triclinic space group Poverline{1} with Jahn–Teller-distorted octa­hedral copper(II) aqua complexes on the centers of inversion. As in (I), the carboxyl­ate group on the anion is protonated and the structure consists of alternating layers of inorganic cations and organic anions linked by O—H⋯O hydrogen bonds. A reaction of silver nitrate and potassium 4-sulfo­benzoic acid in water also resulted in two distinct products that have been structurally characterized. An anhydrous silver potassium 4-carb­oxy­benzene­sulfonate salt, [Ag0.69K0.31](O3SC6H4CO2H), (III), crystallizes in the monoclinic space group C2/c. There are two independent metal sites, one fully occupied by silver ions and the other showing a 62% K+/38% Ag+ (fixed) ratio, refined in two slightly different positions. The coordination environments of the metal ions are composed primarily of sulfonate O atoms, with some participation by the non-protonated carboxyl­ate O atoms in the disordered site. As in the copper compounds, the cations and anions cleanly segregate into alternating layers. A hydrated mixed silver potassium 4-carb­oxy­benzene­sulfonate salt dihydrate, [Ag0.20K0.80](O3SC6H4CO2H)·2H2O, (IV), crystallizes in the monoclinic space group P21/c with the Ag+ and K+ ions sharing one unique metal site coordinated by two water mol­ecules and six sulfonate O atoms. The packing in (IV) follows the dominant motif of alternating inorganic and organic layers. The protonated carboxyl­ate groups do not inter­act with the cations directly, but do participate in hydrogen bonds with the coordinated water mol­ecules. (IV) is isostructural with pure potassium 4-sulfo­benzoic acid dihydrate.

The title compound, C9H7.5NO·C7H3.5ClNO4, was analysed as a disordered structure over two states, viz. co-crystal and salt, accompanied by a keto–enol tautomerization in the base mol­ecule. The co-crystal is 4-chloro-2-nitro­benzoic acid–quinolin-4(1H)-one (1/1), C7H4ClNO4·C9H7NO, and the salt is 4-hy­droxy­quinolinium 4-chloro-2-nitro­benzoate, C9H8NO+·C7H3ClNO4−. In the compound, the acid and base mol­ecules are held together by a short hydrogen bond [O⋯O = 2.4393 (15) Å], in which the H atom is disordered over two positions with equal occupancies. In the crystal, the hydrogen-bonded acid–base units are linked by N—H⋯O and C—H⋯O hydrogen bonds, forming a tape structure along the a-axis direction. The tapes are stacked into a layer parallel to the ab plane via π–π inter­actions [centroid–centroid distances = 3.5504 (8)–3.9010 (11) Å]. The layers are further linked by another C—H⋯O hydrogen bond, forming a three-dimensional network. Hirshfeld surfaces for the title compound mapped over shape-index and dnorm were generated to visualize the inter­molecular inter­actions.

The title pyridazinone derivative, C20H18N2O3, is not planar. The phenyl ring and the pyridazine ring are inclined to each other by 10.55 (12)°, whereas the 4-methyl­benzyl ring is nearly orthogonal to the pyridazine ring, with a dihedral angle of 72.97 (10)°. In the crystal, mol­ecules are linked by pairs of O—H⋯O hydrogen bonds, forming inversion dimers with an R22(14) ring motif. The dimers are linked by C—H⋯O hydrogen bonds, generating ribbons propagating along the c-axis direction. The inter­molecular inter­actions were additionally investigated using Hirshfeld surface analysis and two-dimensional fingerprint plots. They revealed that the most significant contributions to the crystal packing are from H⋯H (48.4%), H⋯O/O⋯H (21.8%) and H⋯C/C⋯H (20.4%) contacts. Mol­ecular orbital calculations providing electron-density plots of HOMO and LUMO mol­ecular orbitals and mol­ecular electrostatic potentials (MEP) were also computed, both with the DFT/B3LYP/6–311 G++(d,p) basis set.

In the mol­ecule of the title anthracene derivative, C22H17NO2, the benzene ring is inclined to the mean plane of the anthracene ring system (r.m.s. deviation = 0.024 Å) by 75.21 (9)°. In the crystal, mol­ecules are linked by pairs of O—H⋯O hydrogen bonds, forming classical carb­oxy­lic acid inversion dimers with an R22(8) ring motif. The dimers are linked by C—H⋯π inter­actions, forming a supra­molecular framework.

In 2,2,5-trimethyl-1,3-dioxane-5-carb­oxy­lic acid, C8H14O4, the carboxyl group occupies an equatorial position on the 1,3-dioxane ring. In the crystal, O—H⋯O hydrogen bonds form chains of mol­ecules, which are linked into a three-dimensional network by C—H⋯O hydrogen bonds. The asymmetric unit of 2,2,5-trimethyl-1,3-dioxane-5-carb­oxy­lic anhydride, C16H26O7, consists of two independent mol­ecules, which are linked by C—H⋯O hydrogen bonds. In the crystal, these units are connected into corrugated layers two mol­ecules thick and parallel to the ab plane by additional C—H⋯O hydrogen bonds.

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.

A copper(II) dimer with the deprotonated anion of 2-bromo­nicotinic acid (2-BrnicH), namely, tetrakis(μ-2-bromonicotinato-κ2O:O')bis[aquacopper(­II)](Cu—Cu), [Cu2(H2O)2(C6H3BrNO2)4] or [Cu2(H2O)2(2-Brnic)4], (1), was prepared by the reaction of copper(II) chloride dihydrate and 2-bromo­nicotinic acid in water. The copper(II) ion in 1 has a distorted square-pyramidal coordination environment, achieved by four carboxyl­ate O atoms in the basal plane and the water mol­ecule in the apical position. The pair of symmetry-related copper(II) ions are connected into a centrosymmetric paddle-wheel dinuclear cluster [Cu⋯Cu = 2.6470 (11) Å] via four O,O'-bridging 2-bromo­nicotinate ligands in the syn-syn coordination mode. In the extended structure of 1, the cluster mol­ecules are assembled into an infinite two-dimensional hydrogen-bonded network lying parallel to the (001) plane via strong O—H⋯O and O—H⋯N hydrogen bonds, leading to the formation of various hydrogen-bond ring motifs: dimeric R22(8) and R22(16) loops and a tetra­meric R44(16) loop. The Hirshfeld surface analysis was also performed in order to better illustrate the nature and abundance of the inter­molecular contacts in the structure of 1.

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.

The title compound, {[Ba7(C3H5O2)14]·0.946C3H6O2·4H2O}n, is represented by a metal–organic framework structure that is held together by Ba—O—Ba bonds, as well as by O—H⋯O hydrogen bonds of moderate strength. The structure comprises of four independent Ba2+ cations (one of which is situated on a twofold rotation axis), seven independent propionate and two independent water mol­ecules. The bond-valence sums of all the cations indicate a slight overbonding. There is also an occupationally, as well as a positionally disordered propionic acid mol­ecule present in the structure. Its occupation is slightly lower than the full occupation while the disordered mol­ecules occupy two positions related by a rotation about a twofold rotation axis. In addition, the methyl group in the symmetry-independent propionic acid mol­ecule is also disordered, and occupies two positions. Each propionic acid mol­ecule coordinates to just one cation from a pair of symmetry-equivalent Ba2+ sites and is simultaneously bonded by an O—H⋯Opropionate hydrogen bond. This means that on a microscopic scale, the coordination number of the corresponding Ba2+ site is either 9 or 10. The methyl as well as hy­droxy hydrogen atoms of the disordered propionic acid mol­ecule were not determined.

Two polymorphs of the title compound, C19H16N2O3, were obtained from ethano­lic (polymorph I) and methano­lic solutions (polymorph II), respectively. Both polymorphs crystallize in the monoclinic system with four formula units per cell and a complete mol­ecule in the asymmetric unit. The main difference between the mol­ecules of (I) and (II) is the reversed position of the hy­droxy group of the carb­oxy­lic function. All other conformational features are found to be similar in the two mol­ecules. The different orientation of the OH group results in different hydrogen-bonding schemes in the crystal structures of (I) and (II). Whereas in (I) inter­molecular O—H⋯O hydrogen bonds with the pyridazinone carbonyl O atom as acceptor generate chains with a C(7) motif extending parallel to the b-axis direction, in the crystal of (II) pairs of inversion-related O—H⋯O hydrogen bonds with an R22(8) ring motif between two carb­oxy­lic functions are found. The inter­molecular inter­actions in both crystal structures were analysed using Hirshfeld surface analysis and two-dimensional fingerprint plots.

The title compound, a major animal feed supplement, abbreviated as HMTBA and alternatively called dl-me­thio­nine hy­droxy analogue, C5H10O3S, (I), was isolated in pure anhydrous monomeric form. The melting point is 302.5 K and the compound crystallizes in the monoclinic space group P21/c, with two conformationally non-equivalent mol­ecules [(IA) and (IB)] in the asymmetric unit. The crystal structure is formed by alternating polar and non-polar layers running along the bc plane and features an extensive hydrogen-bonding network within the polar layers. The Hirshfeld surface analysis revealed a significant contribution of non-polar H⋯H and H⋯S inter­actions to the packing forces for both mol­ecules.

4-[(Morpholin-4-yl)carbothioyl]benzoic acid, C12H13NO3S, a novel phen­yl(morpholino)methane­thione derivative, crystallizes in the monoclinic space group P21/n. The morpholine ring adopts a chair conformation and the carb­oxy­lic acid group is bent out slightly from the benzene ring mean plane. The mol­ecular geometry of the carb­oxy­lic group is characterized by similar C—O bond lengths [1.266 (2) and 1.268 (2) Å] as the carboxyl­ate H atom is disordered over two positions. This mol­ecular arrangement leads to the formation of dimers through strong and centrosymmetric low barrier O—H⋯O hydrogen bonds between the carb­oxy­lic groups. In addition to these inter­molecular inter­actions, the crystal packing consists of two different mol­ecular sheets with an angle between their mean planes of 64.4 (2)°. The cohesion between the different layers is ensured by C—H⋯S and C—H⋯O inter­actions.

The title compound, C22H17NO2·C3H7NO, was synthesized by condensation of an aromatic aldehyde with a secondary amine and subsequent reduction. It was crystallized from a di­methyl­formamide solution as a monosolvate, C22H17NO2·C3H7NO. The aromatic mol­ecule is non-planar with a dihedral angle between the mean planes of the aniline moiety and the methyl anthracene moiety of 81.36 (8)°. The torsion angle of the Car­yl—CH2—NH—Car­yl backbone is 175.9 (2)°. The crystal structure exhibits a three-dimensional supra­molecular network, resulting from hydrogen-bonding inter­actions between the carb­oxy­lic OH group and the solvent O atom as well as between the amine functionality and the O atom of the carb­oxy­lic group and additional C—H⋯π inter­actions. Hirshfeld surface analysis was performed to qu­antify the inter­molecular inter­actions.

The class B family of G-protein-coupled receptors (GPCRs) has long been a paradigm for peptide hormone recognition and signal transduction. One class B GPCR, the glucagon-like peptide-1 receptor (GLP-1R), has been considered as an anti-diabetes drug target and there are several peptidic drugs available for the treatment of this overwhelming disease. The previously determined structures of inactive GLP-1R in complex with two negative allosteric modulators include ten thermal-stabilizing mutations that were selected from a total of 98 designed mutations. Here we systematically summarize all 98 mutations we have tested and the results suggest that the mutagenesis strategy that strengthens inter-helical hydro­phobic interactions shows the highest success rate. We further investigate four back mutations by thermal-shift assay, crystallization and molecular dynamic simulations, and conclude that mutation I1962.66bF increases thermal stability intrinsically and that mutation S2714.47bA decreases crystal packing entropy extrinsically, while mutations S1932.63bC and M2333.36bC may be dispensable since these two cysteines are not di­sulfide-linked. Our results indicate intrinsic connections between different regions of GPCR transmembrane helices and the current data suggest a general mutagenesis principle for structural determination of GPCRs and other membrane proteins.

The non-steroidal anti-inflammatory drugs mefenamic acid (MFA) and tolfenamic acid (TFA) have a close resemblance in their molecular scaffold, whereby a methyl group in MFA is substituted by a chloro group in TFA. The present study demonstrates the isomorphous nature of these compounds in a series of their multicomponent solids. Furthermore, the unique nature of MFA and TFA has been demonstrated while excavating their alternate solid forms in that, by varying the drug (MFA or TFA) to coformer [4-di­methyl­amino­pyridine (DMAP)] stoichiometric ratio, both drugs have produced three different types of multicomponent crystals, viz. salt (1:1; API to coformer ratio), salt hydrate (1:1:1) and cocrystal salt (2:1). Interestingly, as anticipated from the close similarity of TFA and MFA structures, these multicomponent solids have shown an isomorphous relation. A thorough characterization and structural investigation of the new multicomponent forms of MFA and TFA revealed their similarity in terms of space group and structural packing with isomorphic nature among the pairs. Herein, the experimental results are generalized in a broader perspective for predictably identifying any possible new forms of comparable compounds by mapping their crystal structure landscapes. The utility of such an approach is evident from the identification of polymorph VI of TFA from hetero-seeding with isomorphous MFA form I from acetone–methanol (1:1) solution. That aside, a pseudopolymorph of TFA with di­methyl­formamide (DMF) was obtained, which also has some structural similarity to that of the solvate MFA:DMF. These new isostructural pairs are discussed in the context of solid form screening using structural landscape similarity.

Single-particle electron cryo-microscopy (cryoEM) has undergone a `resolution revolution' that makes it possible to characterize megadalton (MDa) complexes at atomic resolution without crystals. To fully exploit the new opportunities in molecular microscopy, new procedures for the cloning, expression and purification of macromolecular complexes need to be explored. Macromolecular assemblies are often unstable, and invasive construct design or inadequate purification conditions and sample-preparation methods can result in disassembly or denaturation. The structure of the 2.6 MDa yeast fatty acid synthase (FAS) has been studied by electron microscopy since the 1960s. Here, a new, streamlined protocol for the rapid production of purified yeast FAS for structure determination by high-resolution cryoEM is reported. Together with a companion protocol for preparing cryoEM specimens on a hydrophilized graphene layer, the new protocol yielded a 3.1 Å resolution map of yeast FAS from 15 000 automatically picked particles within a day. The high map quality enabled a complete atomic model of an intact fungal FAS to be built.

During single-crystal-to-single-crystal (SCSC) phase transitions, a polymorph of a compound can transform to a more stable form while remaining in the solid state. By understanding the mechanism of these transitions, strategies can be developed to control this phenomenon. This is particularly important in the pharmaceutical industry, but also relevant for other industries such as the food and agrochemical industries. Although extensive literature exists on SCSC phase transitions in inorganic crystals, it is unclear whether their classications and mechanisms translate to molecular crystals, with weaker interactions and more steric hindrance. A comparitive study of SCSC phase transitions in aliphatic linear-chain amino acid crystals, both racemates and quasi-racemates, is presented. A total of 34 transitions are considered and most are classified according to their structural change during the transition. Transitions without torsional changes show very different characteristics, such as transition temperature, enthalpy and free energy, compared with transitions that involve torsional changes. These differences can be rationalized using classical nucleation theory and in terms of a difference in mechanism; torsional changes occur in a molecule-by-molecule fashion, whereas transitions without torsional changes involve cooperative motion with multiple molecules at the same time.

Herein the nucleation pathway of conformational polymorphs was revealed by studying the relationships and distinctions among a series of α,ω-alkanedicarboxylic acids [HOOC–(CH2)n−2–COOH, named DAn, where n = 5, 7, 9, 11, 13, 15] in the solid state and in solution. Their polymorphic outcomes, with the exception of DA5, show solvent dependence: form I with conformation I crystallizes from solvents with hydrogen-bond donating (HBD) ability, whereas form II with conformation II crystallizes preferentially from solvents with no HBD ability. In contrast, form II of DA5 does not crystallize in any of the solvents used. Quantum mechanical computation showed that there is no direct conformational link between the solvents and the resultant polymorphic outcomes. Surprisingly, solute aggregates were found in no-HBD solvents by Fourier transform infrared spectroscopy, and only monomers could be detected in HBD solvents, suggesting stronger solvation. Furthermore, it was found that all six compounds including DA5 followed the same pattern in solution. Moreover, crystal-packing efficiency calculations and stability tests stated that dimorphs of DA5 bear a greater stability difference than others. These suggest that the rearrangement from conformation II to I could not be limited by hard desolvation in HBD solvents, where form I was also obtained. In other systems, metastable II was produced in the same solvents, probably as a result of the rearrangement being limited by hard desolvation. In this work, a comparative study uncovers the proposed nucleation pathway: difficulty in desolvation has a remarkable effect on the result of rearrangement and nucleation outcome.

Recent improvements in direct electron detectors, microscope technology and software provided the stimulus for a `quantum leap' in the application of cryo-electron microscopy in structural biology, and many national and international centres have since been created in order to exploit this. Here, a new facility for cryo-electron microscopy focused on single-particle reconstruction of biological macromolecules that has been commissioned at the European Synchrotron Radiation Facility (ESRF) is presented. The facility is operated by a consortium of institutes co-located on the European Photon and Neutron Campus and is managed in a similar fashion to a synchrotron X-ray beamline. It has been open to the ESRF structural biology user community since November 2017 and will remain open during the 2019 ESRF–EBS shutdown.

p-Hydroxymandelate oxidase (Hmo) is a flavin mononucleotide (FMN)-dependent enzyme that oxidizes mandelate to benzoylformate. How the FMN-dependent oxidation is executed by Hmo remains unclear at the molecular level. A continuum of snapshots from crystal structures of Hmo and its mutants in complex with physiological/nonphysiological substrates, products and inhibitors provides a rationale for its substrate enantioselectivity/promiscuity, its active-site geometry/reactivity and its direct hydride-transfer mechanism. A single mutant, Y128F, that extends the two-electron oxidation reaction to a four-electron oxidative decarboxylation reaction was unexpectedly observed. Biochemical and structural approaches, including biochemistry, kinetics, stable isotope labeling and X-ray crystallo­graphy, were exploited to reach these conclusions and provide additional insights.

The Y128F single mutant of p-hydroxymandelate oxidase (Hmo) is capable of oxidizing mandelate to benzoate via a four-electron oxidative decarboxylation reaction. When benzoylformate (the product of the first two-electron oxidation) and hydrogen peroxide (an oxidant) were used as substrates the reaction did not proceed, suggesting that free hydrogen peroxide is not the committed oxidant in the second two-electron oxidation. How the flavin mononucleotide (FMN)-dependent four-electron oxidation reaction takes place remains elusive. Structural and biochemical explorations have shed new light on this issue. 15 high-resolution crystal structures of Hmo and its mutants liganded with or without a substrate reveal that oxidized FMN (FMNox) possesses a previously unknown electrophilic/nucleophilic duality. In the Y128F mutant the active-site perturbation ensemble facilitates the polarization of FMNox to a nucleophilic ylide, which is in a position to act on an α-ketoacid, forming an N5-acyl-FMNred dead-end adduct. In four-electron oxidation, an intramolecular disproportion­ation reaction via an N5-alkanol-FMNred C'α carbanion intermediate may account for the ThDP/PLP/NADPH-independent oxidative decarboxylation reaction. A synthetic 5-deaza-FMNox cofactor in combination with an α-hydroxyamide or α-ketoamide biochemically and structurally supports the proposed mechanism.

As part of the Virus-X Consortium that aims to identify and characterize novel proteins and enzymes from bacteriophages and archaeal viruses, the genes of the putative lytic proteins XepA from Bacillus subtilis prophage PBSX and YomS from prophage SPβ were cloned and the proteins were subsequently produced and functionally characterized. In order to elucidate the role and the molecular mechanism of XepA and YomS, the crystal structures of these proteins were solved at resolutions of 1.9 and 1.3 Å, respectively. XepA consists of two antiparallel β-sandwich domains connected by a 30-amino-acid linker region. A pentamer of this protein adopts a unique dumbbell-shaped architecture consisting of two discs and a central tunnel. YomS (12.9 kDa per monomer), which is less than half the size of XepA (30.3 kDa), shows homology to the C-terminal part of XepA and exhibits a similar pentameric disc arrangement. Each β-sandwich entity resembles the fold of typical cytoplasmic membrane-binding C2 domains. Only XepA exhibits distinct cytotoxic activity in vivo, suggesting that the N-terminal pentameric domain is essential for this biological activity. The biological and structural data presented here suggest that XepA disrupts the proton motive force of the cytoplasmatic membrane, thus supporting cell lysis.

Cryo-electron microscopy (cryo-EM) has rapidly expanded with the introduction of direct electron detectors, improved image-processing software and automated image acquisition. Its recent adoption by industry, particularly in structure-based drug design, creates new requirements in terms of reliability, reproducibility and throughput. In 2016, Thermo Fisher Scientific (then FEI) partnered with the Medical Research Council Laboratory of Molecular Biology, the University of Cambridge Nanoscience Centre and five pharmaceutical companies [Astex Pharmaceuticals, AstraZeneca, GSK, Sosei Heptares and Union Chimique Belge (UCB)] to form the Cambridge Pharmaceutical Cryo-EM Consortium to share the risks of exploring cryo-EM for early-stage drug discovery. The Consortium expanded with a second Themo Scientific Krios Cryo-EM at the University of Cambridge Department of Materials Science and Metallurgy. Several Consortium members have set up in-house facilities, and a full service cryo-EM facility with Krios and Glacios has been created with the Electron Bio-Imaging Centre for Industry (eBIC for Industry) at Diamond Light Source (DLS), UK. This paper will cover the lessons learned during the setting up of these facilities, including two Consortium Krios microscopes and preparation laboratories, several Glacios microscopes at Consortium member sites, and a Krios and Glacios at eBIC for Industry, regarding site evaluation and selection for high-resolution cryo-EM microscopes, the installation process, scheduling, the operation and maintenance of the microscopes and preparation laboratories, and image processing.

As one of the most important phenomena in crystallization, the crystal nucleation process has always been the focus of research. In this work, influences of pre-assembly species and the desolvation process on the crystal nucleation process were studied. p-Nitro­benzoic acid (PNBA) was taken as a model compound to investigate the relationship between solution chemistry and nucleation kinetics in seven different solvents. One unsolvated form and four solvates of PNBA were obtained and one of the solvates was newly discovered. The nucleation behaviours and nucleation kinetics of PNBA in the seven solvents were studied and analyzed. Density functional theory (DFT) and solvation energy calculation were adopted to evaluate the strength of solute–solvent interactions. Vibrational spectroscopy combined with molecular simulation was applied to reveal the pre-assembly species in the solution. Based on these results, a comprehensive understanding of the relationship between molecular structure, crystal structure, solution chemistry and nucleation dynamics was proposed and discussed. It was found that the structural similarity between solution chemistry and crystal structure, the interaction between specific sites and the overall strength of solvation will jointly affect the nucleation process.