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On the structure refinement of metal complexes against 3D electron diffraction data using multipolar scattering factors

This study examines various methods for modelling the electron density and, thus, the electrostatic potential of an organometallic complex for use in crystal structure refinement against 3D electron diffraction (ED) data. It focuses on modelling the scattering factors of iron(III), considering the electron density distribution specific for coordination with organic linkers. We refined the structural model of the metal–organic complex, iron(III) acetyl­acetonate (FeAcAc), using both the independent atom model (IAM) and the transferable aspherical atom model (TAAM). TAAM refinement initially employed multipolar parameters from the MATTS databank for acetyl­acetonate, while iron was modelled with a spherical and neutral approach (TAAM ligand). Later, custom-made TAAM scattering factors for Fe—O coordination were derived from DFT calculations [TAAM-ligand-Fe(III)]. Our findings show that, in this compound, the TAAM scattering factor corresponding to Fe3+ has a lower scattering amplitude than the Fe3+ charged scattering factor described by IAM. When using scattering factors corresponding to the oxidation state of iron, IAM inaccurately represents electrostatic potential maps and overestimates the scattering potential of the iron. In addition, TAAM significantly improved the fitting of the model to the data, shown by improved R1 values, goodness-of-fit (GooF) and reduced noise in the Fourier difference map (based on the residual distribution analysis). For 3D ED, R1 values improved from 19.36% (IAM) to 17.44% (TAAM-ligand) and 17.49% (TAAM-ligand-Fe3+), and for single-crystal X-ray diffraction (SCXRD) from 3.82 to 2.03% and 1.98%, respectively. For 3D ED, the most significant R1 reductions occurred in the low-resolution region (8.65–2.00 Å), dropping from 20.19% (IAM) to 14.67% and 14.89% for TAAM-ligand and TAAM-ligand-Fe(III), respectively, with less improvement in high-resolution ranges (2.00–0.85 Å). This indicates that the major enhancements are due to better scattering modelling in low-resolution zones. Furthermore, when using TAAM instead of IAM, there was a noticeable improvement in the shape of the thermal ellipsoids, which more closely resembled those of an SCXRD-refined model. This study demonstrates the applicability of more sophisticated scattering factors to improve the refinement of metal–organic complexes against 3D ED data, suggesting the need for more accurate modelling methods and highlighting the potential of TAAM in examining the charge distribution of large molecular structures using 3D ED.




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Solvent organization in the ultrahigh-resolution crystal structure of crambin at room temperature

Ultrahigh-resolution structures provide unprecedented details about protein dynamics, hydrogen bonding and solvent networks. The reported 0.70 Å, room-temperature crystal structure of crambin is the highest-resolution ambient-temperature structure of a protein achieved to date. Sufficient data were collected to enable unrestrained refinement of the protein and associated solvent networks using SHELXL. Dynamic solvent networks resulting from alternative side-chain conformations and shifts in water positions are revealed, demonstrating that polypeptide flexibility and formation of clathrate-type structures at hydro­phobic surfaces are the key features endowing crambin crystals with extraordinary diffraction power.




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A predicted model-aided one-step classification–multireconstruction algorithm for X-ray free-electron laser single-particle imaging

Ultrafast, high-intensity X-ray free-electron lasers can perform diffraction imaging of single protein molecules. Various algorithms have been developed to determine the orientation of each single-particle diffraction pattern and reconstruct the 3D diffraction intensity. Most of these algorithms rely on the premise that all diffraction patterns originate from identical protein molecules. However, in actual experiments, diffraction patterns from multiple different molecules may be collected simultaneously. Here, we propose a predicted model-aided one-step classification–multireconstruction algorithm that can handle mixed diffraction patterns from various molecules. The algorithm uses predicted structures of different protein molecules as templates to classify diffraction patterns based on correlation coefficients and determines orientations using a correlation maximization method. Tests on simulated data demonstrated high accuracy and efficiency in classification and reconstruction.




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From formulation to structure: 3D electron diffraction for the structure solution of a new indomethacin polymorph from an amorphous solid dispersion

3D electron diffraction (3DED) is increasingly employed to determine molec­ular and crystal structures from micro-crystals. Indomethacin is a well known, marketed, small-molecule non-steroidal anti-inflammatory drug with eight known polymorphic forms, of which four structures have been elucidated to date. Using 3DED, we determined the structure of a new ninth polymorph, σ, found within an amorphous solid dispersion, a product formulation sometimes used for active pharmaceutical ingredients with poor aqueous solubility. Subsequently, we found that σ indomethacin can be produced from direct solvent evaporation using di­chloro­methane. These results demonstrate the relevance of 3DED within drug development to directly probe product formulations.




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Tuning structural modulation and magnetic properties in metal–organic coordination polymers [CH3NH3]CoxNi1−x(HCOO)3

Three solid solutions of [CH3NH3]CoxNi1−x(HCOO)3, with x = 0.25 (1), x = 0.50 (2) and x = 0.75 (3), were synthesized and their nuclear structures and magnetic properties were characterized using single-crystal neutron diffraction and magnetization measurements. At room temperature, all three compounds crystallize in the Pnma orthorhombic space group, akin to the cobalt and nickel end series members. On cooling, each compound undergoes a distinct series of structural transitions to modulated structures. Compound 1 exhibits a phase transition to a modulated structure analogous to the pure Ni compound [Cañadillas-Delgado, L., Mazzuca, L., Fabelo, O., Rodríguez-Carvajal, J. & Petricek, V. (2020). Inorg. Chem. 59, 17896–17905], whereas compound 3 maintains the behaviour observed in the pure Co compound reported previously [Canadillas-Delgado, L., Mazzuca, L., Fabelo, O., Rodriguez-Velamazan, J. A. & Rodriguez-Carvajal, J. (2019). IUCrJ, 6, 105–115], although in both cases the temperatures at which the phase transitions occur differ slightly from the pure phases. Monochromatic neutron diffraction measurements showed that the structural evolution of 2 diverges from that of either parent compound, with competing hydrogen bond interactions that drive the modulation throughout the series, producing a unique sequence of phases. It involves two modulated phases below 96 (3) and 59 (3) K, with different q vectors, similar to the pure Co compound (with modulated phases below 128 and 96 K); however, it maintains the modulated phase below magnetic order [at 22.5 (7) K], resembling the pure Ni compound (which presents magnetic order below 34 K), resulting in an improper modulated magnetic structure. Despite these large-scale structural changes, magnetometry data reveal that the bulk magnetic properties of these solid solutions form a linear continuum between the end members. Notably, doping of the metal site in these solid solutions allows for tuning of bulk magnetic properties, including magnetic ordering temperature, transition temperatures and the nature of nuclear phase transitions, through adjustment of metal ratios.




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Lattice response to the radiation damage of molecular crystals: radiation-induced versus thermal expansivity

The interaction of intense synchrotron radiation with molecular crystals frequently modifies the crystal structure by breaking bonds, producing fragments and, hence, inducing disorder. Here, a second-rank tensor of radiation-induced lattice strain is proposed to characterize the structural susceptibility to radiation. Quantitative estimates are derived using a linear response approximation from experimental data collected on three materials Hg(NO3)2(PPh3)2, Hg(CN)2(PPh3)2 and BiPh3 [PPh3 = triphenylphosphine, P(C6H5)3; Ph = phenyl, C6H5], and are compared with the corresponding thermal expansivities. The associated eigenvalues and eigenvectors show that the two tensors are not the same and therefore probe truly different structural responses. The tensor of radiative expansion serves as a measure of the susceptibility of crystal structures to radiation damage.




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Three-dimensional electron diffraction on clinkers: the belite α'H incommensurate modulated structure

Traditional X-ray methods are extensively applied to commercial cement samples in order to determine their physical and chemical properties. Powder patterns are routinely used to quantify the composition of these phase mixtures, but structure determination becomes difficult because of reflection overlapping caused by the high number of different crystal structures. The fast-growing 3D electron diffraction technique and its related automated acquisition protocols arise as a potentially very interesting tool for the cement industry, since they enable the fast and systematic acquisition of diffraction data from individual particles. In this context, electron diffraction has been used in the investigation of the different crystalline phases present in various commercial clinkers for cement. Automated data collection procedures and subsequent data processing have enabled the structural characterization of the different crystal structures from which the α'H polymorph of Ca2SiO4 (belite) exhibited satellite reflections. Its average crystal structure has been known since 1971 and satellite reflections have been reported previously, yet the modulation was never fully described by means of the superspace formalism. Here, the incommensurately modulated structure is solved and refined using harmonic and crenel functions in the superspace group Pnma(α00)0ss, showing the potential of 3D electron diffraction for systematic crystallographic characterizations of cement. A full description of the different belite polymorphs is provided considering this modulated structure.




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Attractive and repulsive forces in a crystal of [Rb(18-crown-6)][SbCl6] under high pressure

The compression behavior of [Rb(18-crown-6)][SbCl6] crystal under pressure up to 2.16 (3) GPa was investigated in a diamond anvil cell (DAC) using a mixture of pentane–iso­pentane (1:4) as the pressure-transmitting fluid. The compound crystallizes in trigonal space group R3 and no phase transition was observed in the indicated pressure range. The low value of pressure bulk modulus [9.1 (5) GPa] found in this crystal is a characteristic of soft materials with predominant dispersive and electrostatic interaction forces. The nonlinear relationship between unit-cell parameters under high pressure is attributed to the influence of reduced intermolecular H⋯Cl contacts under pressure over 0.73 GPa. It also explains the high compression efficiency of [Rb(18-crown-6)][SbCl6] crystals at relatively low pressures, resulting in a significant shift of the Rb atom to the center of the crown ether cavity. At pressures above 0.9 GPa, steric repulsion forces begin to play a remarkable role, since an increasing number of interatomic H⋯Cl and H⋯H contacts become shorter than the sum of their van der Waals (vdW) radii. Below 0.9 GPa, both unit-cell parameter dependences (P–a and P–c) exhibit hysteresis upon pressure release, demonstrating their influence on the disordered model of Rb atoms. The void reduction under pressure also demonstrates two linear sections with the inflection point at 0.9 GPa. Compression of the crystal is accompanied by a significant decrease in the volume of the voids, leading to the rapid approach of Rb atoms to the center of the crown ether cavity. For the Rb atom to penetrate into the center of the crown ether cavity in [Rb(18-crown-6)][SbCl6], it is necessary to apply a pressure of about 2.5 GPa to disrupt the balance of atomic forces in the crystal. This sample serves as a compression model demonstrating the influence of both attractive and repulsive forces on the change in unit-cell parameters under pressure.




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Supramolecular synthons in hydrates and solvates of lamotrigine: a tool for cocrystal design

The molecule of anti-epileptic drug lamotrigine [LAM; 3,5-diamino-6-(2,3-dichlorophenyl)-1,2,4-triazine] is capable of the formation of multicomponent solids. Such an enhanced tendency is related to the diverse functionalities of the LAM chemical groups able to form hydrogen bonds. Two robust synthons are recognized in the supramolecular structure of LAM itself formed via N—H⋯N hydrogen bond: homosynthon, so-called aminopyridine dimer or synthon 1 [R22(8)] and larger homosynthon 2 [R32(8)]. The synthetic procedures for a new hydrate and 11 solvates of LAM (in the series: with acetone, ethanol: two polymorphs: form I and form II, 2-propanol, n-butanol, tert-butanol, n-pentanol, benzonitrile, acetonitrile, DMSO and dioxane) were performed. The comparative solid state structural analysis of a new hydrate and 11 solvates of LAM has been undertaken in order to establish robustness of the supramolecular synthons 1 and 2 found in the crystal structure of LAM itself as well as LAM susceptibility to build methodical solid state supramolecular architecture in the given competitive surrounding of potential hydrogen bonds. The aminopyridine dimer homosynthon 1 [R22(8)] has been switched from para-para (P-P) topology to ortho-ortho (O-O) topology in all crystal structures, except in LAM:n-pentanol:water solvate where it remains P-P. Homosynthon 2 [R32(8)] of the LAM crystal structure imitates in the LAM solvates as a heterosynthon by replacing the triazine nitrogen proton acceptor atoms of LAM with the proton acceptors of solvates molecules.




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Supramolecular architectures in multicomponent crystals of imidazole-based drugs and tri­thio­cyanuric acid

The structures of three multicomponent crystals formed with imidazole-based drugs, namely metronidazole, ketoconazole and miconazole, in conjunction with tri­thio­cyanuric acid are characterized. Each of the obtained adducts represents a different category of crystalline molecular forms: a cocrystal, a salt and a cocrystal of salt. The structural analysis revealed that in all cases, the N—H⋯N hydrogen bond is responsible for the formation of acid–base pairs, regardless of whether proton transfer occurs or not, and these molecular pairs are combined to form unique supramolecular motifs by centrosymmetric N—H⋯S interactions between acid molecules. The complex intermolecular forces acting in characteristic patterns are discussed from the geometric and energetic perspectives, involving Hirshfeld surface analysis, pairwise energy estimation, and natural bond orbital calculations.




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Synthesis and properties of Sr2La2NiW2O12, a new S = 1 triangular lattice magnet

Magnetic materials featuring triangular arrangements of spins are frequently investigated as platforms hosting magnetic frustration. Hexagonal perovskites with ordered vacancies serve as excellent candidates for two-dimensional triangular magnetism due to the considerable separation of the magnetic planes. In this work, the effects of chemical pressure on the ferromagnetic ground state of Ba2La2NiW2O12 by substitution of Ba2+ with Sr2+ to produce Sr2La2NiW2O12 are investigated. The two materials are characterized using synchrotron-based XRD, XANES and EXAFS in addition to magnetometry in order to correlate their crystal structures and magnetic properties. Both materials form in space group R3, yet as a result of the enhanced bending of key bond angles due to the effects of chemical pressure, the TC value of the magnetic Ni2+ sublattice is reduced from ∼6 K in Ba2La2NiW2O12 to 4 K in Sr2La2NiW2O12.




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Crystal structure of N-terminally hexahistidine-tagged Onchocerca volvulus macrophage migration inhibitory factor-1

Onchocerca volvulus causes blindness, onchocerciasis, skin infections and devastating neurological diseases such as nodding syndrome. New treatments are needed because the currently used drug, ivermectin, is contraindicated in pregnant women and those co-infected with Loa loa. The Seattle Structural Genomics Center for Infectious Disease (SSGCID) produced, crystallized and determined the apo structure of N-terminally hexahistidine-tagged O. volvulus macrophage migration inhibitory factor-1 (His-OvMIF-1). OvMIF-1 is a possible drug target. His-OvMIF-1 has a unique jellyfish-like structure with a prototypical macrophage migration inhibitory factor (MIF) trimer as the `head' and a unique C-terminal `tail'. Deleting the N-terminal tag reveals an OvMIF-1 structure with a larger cavity than that observed in human MIF that can be targeted for drug repurposing and discovery. Removal of the tag will be necessary to determine the actual biological oligomer of OvMIF-1 because size-exclusion chomatographic analysis of His-OvMIF-1 suggests a monomer, while PISA analysis suggests a hexamer stabilized by the unique C-terminal tails.




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Crystal structure, Hirshfeld surface analysis, inter­molecular inter­action energies, energy frameworks and DFT calculations of 4-amino-1-(prop-2-yn-1-yl)pyrimidin-2(1H)-one

In the title mol­ecule, C7H7N3O, the pyrimidine ring is essentially planar, with the propynyl group rotated out of this plane by 15.31 (4)°. In the crystal, a tri-periodic network is formed by N—H⋯O, N—H⋯N and C—H⋯O hydrogen-bonding and slipped π–π stacking inter­actions, leading to narrow channels extending parallel to the c axis. Hirshfeld surface analysis of the crystal structure reveals that the most important contributions for the crystal packing are from H⋯H (36.2%), H⋯C/C⋯H (20.9%), H⋯O/O⋯H (17.8%) and H⋯N/N⋯H (12.2%) inter­actions, showing that hydrogen-bonding and van der Waals inter­actions are the dominant inter­actions in the crystal packing. Evaluation of the electrostatic, dispersion and total energy frameworks indicates that the stabilization is dominated by the electrostatic energy contributions. The mol­ecular structure optimized by density functional theory (DFT) calculations at the B3LYP/6–311 G(d,p) level is compared with the experimentally determined structure in the solid state. The HOMO–LUMO behaviour was also elucidated to determine the energy gap.




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Synthesis, crystal structure and Hirshfeld surface analysis of a cadmium complex of naphthalene-1,5-di­sulfonate and o-phenyl­enedi­amine

A novel o-phenyl­enedi­amine (opda)-based cadmium complex, bis­(benzene-1,2-di­amine-κ2N,N')bis­(benzene-1,2-di­amine-κN)cadmium(II) naphthalene-1,5-di­sulfonate, [Cd(C6H8N2)4](C10H6O6S2), was synthesized. The complex salt crystallizes in the monoclinic space group C2/c. The Cd atom occupies a special position and coordinates six nitro­gen atoms from four o-phenyl­enedi­amine mol­ecules, two as chelating ligands and two as monodentate ligands. The amino H atoms of opda inter­act with two O atoms of the naphthalene-1,5-di­sulfonate anions. The anions act as bridges between [Cd(opda)4]2+ cations, forming a two-dimensional network in the [010] and [001] directions. The Hirshfeld surface analysis shows that the primary factors contributing to the supramolecular inter­actions are short contacts, particularly van der Waals forces of the type H⋯H, O⋯H and C⋯H.




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Crystal structure of dilithium biphenyl-4,4'-di­sulfonate dihydrate

The asymmetric unit of the title compound, μ-biphenyl-4,4'-di­sulfonato-bis­(aqua­lithium), [Li2(C12H8O6S2)(H2O)2] or Li2[Bph(SO3)2](H2O)2, consists of an Li ion, half of the diphenyl-4,4'-di­sulfonate [Bph(SO3−)2] ligand, and a water mol­ecule. The Li ion exhibits a four-coordinate tetra­hedral geometry with three oxygen atoms of the Bph(SO3−)2 ligands and a water mol­ecule. The tetra­hedral LiO4 units, which are inter­connected by biphenyl moieties, form a layer structure parallel to (100). These layers are further connected by hydrogen-bonding inter­actions to yield a three-dimensional network.




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Crystal structure and Hirshfeld surface analysis of dimethyl 4-hy­droxy-5,4'-dimethyl-2'-(toluene-4-sulfonyl­amino)­biphenyl-2,3-di­carboxyl­ate

In the title compound, C25H25NO7S, the mol­ecular conformation is stabilized by intra­molecular O—H⋯O and N—H⋯O hydrogen bonds, which form S(6) and S(8) ring motifs, respectively. The mol­ecules are bent at the S atom with a C—SO2—NH—C torsion angle of −70.86 (11)°. In the crystal, mol­ecules are linked by C—H⋯O and N—H⋯O hydrogen bonds, forming mol­ecular layers parallel to the (100) plane. C—H⋯π inter­actions are observed between these layers.




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An unexpected tautomer: synthesis and crystal structure of N-[6-amino-4-(methyl­sulfan­yl)-1,2-di­hydro-1,3,5-triazin-2-yl­idene]benzenesulfonamide

The title compound, C10H11N5O2S2, consists of an unexpected tautomer with a protonated nitro­gen atom in the triazine ring and a formal exocyclic double bond C=N to the sulfonamide moiety. The ring angles at the unsubstituted nitro­gen atoms are narrow, at 115.57 (12) and 115.19 (12)°, respectively, whereas the angle at the carbon atom between these N atoms is very wide, 127.97 (13)°. The inter­planar angle between the two rings is 79.56 (5)°. The mol­ecules are linked by three classical hydrogen bonds, forming a ribbon structure. There are also unusual linkages involving three short contacts (< 3 Å) from a sulfonamide oxygen atom to the C—NH—C part of a triazine ring.




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Synthesis and crystal structures of boryl ortho-silylaryl tri­fluoro­methane­sulfonates

We report the synthesis and structural characterization of three crystalline borylated ortho-silylaryl tri­fluoro­methane­sulfonates: 5-(4,4,5,5-tetra­methyl-1,3,2-dioxaborolan-2-yl)-2-(tri­methyl­sil­yl)phenyl tri­fluoro­methane­sulfonate, C16H24BF3O5SSi (1a), 4-(4,4,5,5-tetra­methyl-1,3,2-dioxaborolan-2-yl)-2-(tri­methyl­sil­yl)phenyl tri­fluoro­methane­sulfonate, C16H24BF3O5SSi (1b), and 2-methyl-4-(4,4,5,5-tetra­methyl-1,3,2-dioxaborolan-2-yl)-6-(tri­methyl­silyl)phen­yl tri­fluoro­methane­sulfonate, C17H26BF3O5SSi (2), which are versatile aryne precursors. For all three compounds, the heteroatom substituents are almost coplanar with the central aromatic moiety. C—heteroatom bonding metrics are unexceptional and fall withing the typical range of C—B, C—Si, and C—O single bonds. Despite numerous electronegative sites, only weak inter­molecular inter­actions are observed in the solid state.




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Crystal structure, Hirshfeld surface analysis, crystal voids, inter­action energy calculations and energy frameworks and DFT calculations of ethyl 2-cyano-3-(3-hy­droxy-5-methyl-1H-pyrazol-4-yl)-3-phen­yl­propano­ate

The title compound, C16H17N3O3, is racemic as it crystallizes in a centrosymmetric space group (Poverline{1}), although the trans disposition of substituents about the central C—C bond is established. The five- and six-membered rings are oriented at a dihedral angle of 75.88 (8)°. In the crystal, N—H⋯N hydrogen bonds form chains of mol­ecules extending along the c-axis direction that are connected by inversion-related pairs of O—H⋯N into ribbons. The ribbons are linked by C—H⋯π(ring) inter­actions, forming layers parallel to the ab plane. A Hirshfeld surface analysis indicates that the most important contributions for the crystal packing are from H⋯H (45.9%), H⋯N/N⋯H (23.3%), H⋯C/C⋯H (16.2%) and H⋯O/O⋯H (12.3%) inter­actions. Hydrogen bonding and van der Waals inter­actions are the dominant inter­actions in the crystal packing. The volume of the crystal voids and the percentage of free space were calculated to be 100.94 Å3 and 13.20%, showing that there is no large cavity in the crystal packing. Evaluation of the electrostatic, dispersion and total energy frameworks indicates that the stabilization is dominated by the electrostatic energy contributions in the title compound. Moreover, the DFT-optimized structure at the B3LYP/6–311 G(d,p) level is compared with the experimentally determined mol­ecular structure in the solid state. The HOMO–LUMO behaviour was elucidated to determine the energy gap.




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Crystal structure, Hirshfeld surface analysis, crystal voids, inter­action energy calculations and energy frameworks, and DFT calculations of 1-(4-methyl­benz­yl)in­do­line-2,3-dione

The in­do­line portion of the title mol­ecule, C16H13NO2, is planar. In the crystal, a layer structure is generated by C—H⋯O hydrogen bonds and C—H⋯π(ring), π-stacking and C=O⋯π(ring) inter­actions. The Hirshfeld surface analysis of the crystal structure indicates that the most important contributions for the crystal packing are from H⋯H (43.0%), H⋯C/C⋯H (25.0%) and H⋯O/O⋯H (22.8%) inter­actions. Hydrogen bonding and van der Waals inter­actions are the dominant inter­actions in the crystal packing. The volume of the crystal voids and the percentage of free space were calculated to be 120.52 Å3 and 9.64%, respectively, showing that there is no large cavity in the crystal packing. Evaluation of the electrostatic, dispersion and total energy frameworks indicate that the stabilization is dominated by the dispersion energy contributions in the title compound. Moreover, the DFT-optimized structure at the B3LYP/6-311G(d,p) level is compared with the experimentally determined mol­ecular structure in the solid state.




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Synthesis, crystal structure and Hirshfeld surface analysis of 2-({5-[(naphthalen-1-yl)meth­yl]-4-phenyl-4H-1,2,4-triazol-3-yl}sulfan­yl)-1-(4-nitro­phen­yl)ethanone

The title compound, C27H20N4O3S, crystallizes in the monoclinic system, space group P21/n, with Z = 4. The global shape of the mol­ecule is determined by the orientation of the substituents on the central 4H-1,2,4-triazole ring. The nitro­phenyl ring, phenyl ring, and naphthalene ring system are oriented at dihedral angles of 82.95 (17), 77.14 (18) and 89.46 (15)°, respectively, with respect to the triazole ring. The crystal packing features chain formation in the b-axis direction by S⋯O inter­actions. A Hirshfeld surface analysis indicates that the highest contributions to surface contacts arise from contacts in which H atoms are involved.




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Crystal structures of sulfonamide protected bicyclic guanidines: (S)-8-{[(tert-butyl­dimethyl­sil­yl)­oxy]meth­yl}-1-[(2,2,4,6,7-penta­methyl-2,3-di­hydro­benzo­furan-5-yl)sulfon­yl]-1,3,4,6,7,8-hexa­

Two compounds, (S)-8-{[(tert-butyl­dimethyl­sil­yl)­oxy]meth­yl}-1-[(2,2,4,6,7-penta­methyl-2,3-di­hydro­benzo­furan-5-yl)sulfon­yl]-1,3,4,6,7,8-hexa­hydro-2H-pyrimido[1,2-a]pyrimidin-1-ium tri­fluoro­methane­sulfonate, C27H46N3O4SSi+·CF3O3S−, (1) and (S)-8-(iodo­meth­yl)-1-tosyl-1,3,4,6,7,8-hexa­hydro-2H-pyrimido[1,2-a]pyrimidin-1-ium iodide, C15H21IN3O2S+·I−, (2), have been synthesized and characterized. They are bicyclic guanidinium salts and were synthesized from N-(tert-but­oxy­carbon­yl)-l-me­thio­nine (Boc-l-Met-OH). The guanidine is protected by a 2,2,4,6,7-penta­methyl­dihydro­benzo­furan-5-sulfonyl (Pbf, 1) or a tosyl (2) group. In the crystals of both compounds, the guanidinium group is almost planar and the N–H forms an intra­molecular hydrogen bond in a six-membered ring to the oxygen atom of the sulfonamide protecting group.




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Crystal structure of the tetra­ethyl­ammonium salt of the non-steroidal anti-inflammatory drug nimesulide (polymorph II)

The crystal structure of the tetra­ethyl­ammonium salt of the non-steroidal anti-inflammatory drug nimesulide (polymorph II) (systematic name: tetra­ethyl­ammonium N-methane­sulfonyl-4-nitro-2-phen­oxy­anilinide), C8H20N+·C13H11N2O5S−, was determined using single-crystal X-ray diffraction. The title compound crystallizes in the monoclinic space group P21/c with one tetra­ethyl­ammonium cation and one nimesulide anion in the asymmetric unit. In the crystal, the ions are linked by C—H⋯N and C—H⋯O hydrogen bonds and C—H⋯π inter­actions. There are differences in the geometry of both the nimesulide anion and the tetra­ethyl­ammonium cation in polymorphs I [Rybczyńska & Sikorski (2023). Sci. Rep. 13, 17268] and II of the title compound.




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Crystal structure and Hirshfeld surface analysis of 4-oxo-3-phenyl-2-sulfanyl­idene-5-(thio­phen-2-yl)-3,4,7,8,9,10-hexa­hydro-2H-pyrido[1,6-a:2,3-d']di­pyrimidine-6-carbo­nitrile

In the title compound, C21H15N5OS2, mol­ecular pairs are linked by N—H⋯N hydrogen bonds along the c-axis direction and C—H⋯S and C—H⋯O hydrogen bonds along the b-axis direction, with R22(12) and R22(16) motifs, respectively, thus forming layers parallel to the (10overline{4}) plane. In addition, C=S⋯π and C≡N⋯π inter­actions between the layers ensure crystal cohesion. The Hirshfeld surface analysis indicates that the major contributions to the crystal packing are H⋯H (43.0%), C⋯H/H⋯C (16.9%), N⋯H/H⋯N (11.3%) and S⋯H/H⋯S (10.9%) inter­actions.




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Crystal structure of tetra­kis­(μ-2-hy­droxy-3,5-di­isoprop­yl­benzoato)bis­[(dimethyl sulfoxide)copper(II)]

Metal complexes of 3,5-diiso­propyl­salicylate are reported to have anti-inflammatory and anti-convulsant activities. The title binuclear copper complex, [Cu2(C13H17O3)4(C2H6OS)2] or [Cu(II)2(3,5-DIPS)4(DMSO)2], contains two five-coordinate copper atoms that are bridged by four 3,5-diiso­propyl­salicylate ligands and capped by two axial dimethyl sulfoxide (DMSO) moieties. Each copper atom is attached to four oxygen atoms in an almost square-planar fashion, with the addition of a DMSO ligand in an apical position leading to a square-pyramidal arrangement. The hy­droxy group of the diiso­propyl­salicylate ligands participates in intra­molecular O—H⋯O hydrogen-bonding inter­actions.




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Crystal structure of tetra­phenyl phosphate tetra­kis­[dimethyl (2,2,2-tri­chloro­acet­yl)phos­pho­ramidato]lutetium(III), PPh4[LuL4]

A lutetium(III) complex based on the anion of the ligand dimethyl (2,2,2-tri­chloro­acet­yl)phospho­ramidate (HL) and tetra­phenylphosphonium, of composition PPh4[LuL4] (L = CAPh = carbacyl­amido­phosphate), or (C24H20)[Lu(C4H6Cl3NO4P)4], has been synthesized and structurally characterized. The X-ray diffraction study of the compound revealed that the lutetium ion is surrounded by four bis-chelating CAPh ligands, forming the complex anion [LuL4]− with a coordination number of 8[O] for LuIII, while PPh4+ serves as a counter-ion. The coordination geometry around the Lu3+ ion was determined to be a nearly perfect triangular dodeca­hedron. The complex crystallizes in the monoclinic crystal system, space group P21/c, with four mol­ecules in the unit cell. Weak hydrogen bonds O⋯HC(Ph), Cl⋯HC(Ph) and N⋯HC(Ph) are formed between the cations and anions. For a comparative study, HL-based structures were retrieved from the Cambridge Structural Database (CSD) and their geometries and conformations are discussed. A Hirshfeld surface analysis was also performed.




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Crystal structure and Hirshfeld surface analysis of 8-benzyl-1-[(4-methyl­phen­yl)sulfon­yl]-2,7,8,9-tetra­hydro-1H-3,6:10,13-diep­oxy-1,8-benzodi­aza­cyclo­penta­decine ethanol hemisolvate

The asymmetric unit of the title compound, 2C31H28N2O4S·C2H6O, contains a parent mol­ecule and a half mol­ecule of ethanol solvent. The main compound stabilizes its mol­ecular conformation by forming a ring with an R12(7) motif with the ethanol solvent mol­ecule. In the crystal, mol­ecules are connected by C—H⋯O and O—H⋯O hydrogen bonds, forming a three-dimensional network. In addition, C—H⋯π inter­actions also strengthen the mol­ecular packing.




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Crystal structure, Hirshfeld surface analysis, calculations of crystal voids, inter­action energy and energy frameworks as well as density functional theory (DFT) calculations of 3-[2-(morpholin-4-yl)eth­yl]-5,5-di­phenyl­imidazolidine

In the title mol­ecule, C21H23N3O3, the imidazolidine ring slightly deviates from planarity and the morpholine ring exhibits the chair conformation. In the crystal, N—H⋯O and C—H⋯O hydrogen bonds form helical chains of mol­ecules extending parallel to the c axis that are connected by C—H⋯π(ring) inter­actions. A Hirshfeld surface analysis reveals that the most important contributions for the crystal packing are from H⋯H (55.2%), H⋯C/C⋯H (22.6%) and H⋯O/O⋯H (20.5%) inter­actions. The volume of the crystal voids and the percentage of free space were calculated to be 236.78 Å3 and 12.71%, respectively. Evaluation of the electrostatic, dispersion and total energy frameworks indicates that the stabilization is dominated by the nearly equal electrostatic and dispersion energy contributions. The DFT-optimized mol­ecular structure at the B3LYP/6-311 G(d,p) level is compared with the experimentally determined mol­ecular structure in the solid state. Moreover, the HOMO–LUMO behaviour was elucidated to determine the energy gap.




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Synthesis and crystal structure of N-phenyl-2-(phenyl­sulfan­yl)acetamide

N-Phenyl-2-(phenyl­sulfan­yl)acetamide, C14H13NOS, was synthesized and structurally characterized. In the crystal, N—H⋯O hydrogen bonding leads to the formation of chains of mol­ecules along the [100] direction. The chains are linked by C—H⋯π inter­actions, forming a three-dimensional network. The crystal studied was twinned by a twofold rotation around [100].




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Synthesis, characterization and supra­molecular analysis for (E)-3-(pyridin-4-yl)acrylic acid

The title compound, C8H7NO2, crystallizes as prismatic colourless crystals in space group Poverline{1}, with one mol­ecule in the asymmetric unit. The pyridine ring is fused to acrylic acid, forming an almost planar structure with an E-configuration about the double bond with a torsion angle of −6.1 (2)°. In the crystal, strong O—H⋯N inter­actions link the mol­ecules, forming chains along the [101] direction. Weak C—H⋯O inter­actions link adjacent chains along the [100] direction, generating an R22(14) homosynthon. Finally, π–π stacking inter­actions lead to the formation of the three-dimensional structure. The supra­molecular analysis was supported by Hirshfeld surface and two-dimensional fingerprint plot analysis, indicating that the most abundant contacts are associated with H⋯H, O⋯H/H⋯O, N⋯H/H⋯N and C⋯H/H⋯C inter­actions.




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Synthesis, crystal structure and Hirshfeld surface analysis of bromido­tetra­kis­[5-(prop-2-en-1-yl­sulf­an­yl)-1,3,4-thia­diazol-2-amine-κN3]copper(II) bromide

A novel cationic complex, bromido­tetra­kis­[5-(prop-2-en-1-ylsulfan­yl)-1,3,4-thia­diazol-2-amine-κN3]copper(II) bromide, [CuBr](C5H7N3S2)4Br, was synthesized. The complex crystallizes with fourfold mol­ecular symmetry in the tetra­gonal space group P4/n. The CuII atom exhibits a square-pyramidal coord­ination geometry. The Cu atom is located centrally within the complex, being coordinated by four nitro­gen atoms from four AAT mol­ecules, while a bromine anion is located at the apex of the pyramid. The amino H atoms of AAT inter­act with bromine from the inner and outer spheres, forming a two-dimensional network in the [100] and [010] directions. Hirshfeld surface analysis reveals that 33.7% of the inter­mol­ecular inter­actions are from H⋯H contacts, 21.2% are from S⋯H/H⋯S contacts, 13.4% are from S⋯S contacts and 11.0% are from C⋯H/H⋯C, while other contributions are from Br⋯H/H⋯Br and N⋯H/H⋯N contacts.




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2-Cyano-2-iso­nitro­soacetamide–3,4-di­methylpyrazole (1/1): a co-crystal of two mol­ecules with agrochemical activities

In the structure of the title co-crystal, C3H3N3O2·C5H8N2, the components are linked by a set of directional O—H⋯N, N—H⋯O, N—H⋯N and C—H⋯O hydrogen bonds to yield a two-dimensional mono-periodic arrangement. The structure propagates in the third dimension by extensive π–π stacking inter­actions of nearly parallel mol­ecules of the two components, following an alternating sequence. The primary structure-defining inter­action is very strong oxime-OH donor to pyrazole-N acceptor hydrogen bond [O⋯N = 2.587 (2) Å], while the significance of weaker hydrogen bonds and π–π stacking inter­actions is comparable. The distinct structural roles of different kinds of inter­actions agree with the results of a Hirshfeld surface analysis and calculated inter­action energies. The title compound provides insights into co-crystals of active agrochemical mol­ecules and features the rational integration in one structure of a fungicide, C3H3N3O2, and a second active component, C5H8N2, known for alleviation the toxic effects of fungicides on plants. The material appears to be well suited for practical uses, being non-volatile, air-stable, water-soluble, but neither hygroscopic nor efflorescent.




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Bis[tris­(diiso­butyl­dithio­carbamato)-μ3-sulfido-tri-μ2-di­sulfido-trimolybdenum(IV)] sulfide tetra­hydro­furan monosolvate

The title compound, [Mo3(C9H18NS2)3(S2)3S]2S, crystallizes on a general position in the monoclinic space group P21/n (No. 14). The cationic [Mo3S7(S2CNiBu2)3]+ fragments are joined by a mono­sulfide dianion that forms close S⋯S contacts to each of the di­sulfide ligands on the side of the Mo3 plane opposite the μ32− ligand. The two Mo3 planes are inclined at an angle of 40.637 (15)°, which gives the assembly an open clamshell-like appearance. One μ6-S2−⋯S22− contact, at 2.4849 (14) Å, is appreciably shorter than the remaining five, which are in the range 2.7252 (13)–2.8077 (14) Å.




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Synthesis and crystal structures of N,2,4,6-tetra­methyl­anilinium tri­fluoro­methane­sulfonate and N-iso­propyl­idene-N,2,4,6-tetra­methyl­anilinium tri­fluoro­methane­sulfonate

Two 2,4,6-tri­methyl­aniline-based trifuloro­methane­sulfonate (tri­fluoro­methane­sulfonate) salts were synthesized and characterized by single-crystal X-ray diffraction. N,2,4,6-Tetra­methyl­anilinium tri­fluoro­methane­sulfonate, [C10H14NH2+][CF3O3S−] (1), was synthesized via methyl­ation of 2,4,6-tri­methyl­aniline. N-Iso­propyl­idene-N,2,4,6-tetra­methyl­anilinium tri­fluoro­meth­ane­sulfonate, [C13H20N+][CF3O3S−] (2), was synthesized in a two-step reaction where the imine, N-iso­propyl­idene-2,4,6-tri­methyl­aniline, was first prepared via a dehydration reaction to form the Schiff base, followed by methyl­ation using methyl tri­fluoro­methane­sulfonate to form the iminium ion. In compound 1, both hydrogen bonding and π–π inter­actions form the main inter­molecular inter­actions. The primary inter­action is a strong N—H⋯O hydrogen bond with the oxygen atoms of the tri­fluoro­methane­sulfonate anions bonded to the hydrogen atoms of the ammonium nitro­gen atom to generate a one-dimensional chain. The [C10H14NH2+] cations form dimers where the benzene rings form a π–π inter­action with a parallel-displaced geometry. The separation distance between the calculated centroids of the benzene rings is 3.9129 (8) Å, and the inter­planar spacing and ring slippage between the dimers are 3.5156 (5) and 1.718 Å, respectively. For 2, the [C13H20N+] cations also form dimers as in 1, but with the benzene rings highly slipped. The distance between the calculated centroids of the benzene rings is 4.8937 (8) Å, and inter­planar spacing and ring slippage are 3.3646 (5) and 3.553 Å, respectively. The major inter­molecular inter­actions in 2 are instead a series of weaker C—H⋯O hydrogen bonds [C⋯O distances of 3.1723 (17), 3.3789 (18), and 3.3789 (18) Å], an inter­action virtually absent in the structure of 1. Fluorine atoms are not involved in strong directional inter­actions in either structure.




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Crystal structure characterization, Hirshfeld surface analysis, and DFT calculation studies of 1-(6-amino-5-nitro­naphthalen-2-yl)ethanone

The title compound, C12H10N2O3, was obtained by the de­acetyl­ation reaction of 1-(6-amino-5-nitro­naphthalen-2-yl)ethanone in a concentrated sulfuric acid methanol solution. The mol­ecule comprises a naphthalene ring system bearing an acetyl group (C-3), an amino group (C-7), and a nitro group (C-8). In the crystal, the mol­ecules are assembled into a two-dimensional network by N⋯H/H⋯N and O⋯H/H⋯O hydrogen-bonding inter­actions. n–π and π–π stacking inter­actions are the dominant inter­actions in the three-dimensional crystal packing. Hirshfeld surface analysis indicates that the most important contributions are from O⋯H/H⋯O (34.9%), H⋯H (33.7%), and C⋯H/H⋯C (11.0%) contacts. The energies of the frontier mol­ecular orbitals were computed using density functional theory (DFT) calculations at the B3LYP-D3BJ/def2-TZVP level of theory and the LUMO–HOMO energy gap of the mol­ecule is 3.765 eV.




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Crystal structure, Hirshfeld surface analysis, calculations of inter­molecular inter­action energies and energy frameworks and the DFT-optimized mol­ecular structure of 1-[(1-butyl-1H-1,2,3-triazol-4-yl)meth­yl]-3-(prop-1-en-2-yl)-1H-b

The benzimidazole entity of the title mol­ecule, C17H21N5O, is almost planar (r.m.s. deviation = 0.0262 Å). In the crystal, bifurcated C—H⋯O hydrogen bonds link individual mol­ecules into layers extending parallel to the ac plane. Two weak C—H⋯π(ring) inter­actions may also be effective in the stabilization of the crystal structure. Hirshfeld surface analysis of the crystal structure reveals that the most important contributions for the crystal packing are from H⋯H (57.9%), H⋯C/C⋯H (18.1%) and H⋯O/O⋯H (14.9%) inter­actions. Hydrogen bonding and van der Waals inter­actions are the most dominant forces in the crystal packing. Evaluation of the electrostatic, dispersion and total energy frameworks indicate that the stabilization of the title compound is dominated via dispersion energy contributions. The mol­ecular structure optimized by density functional theory (DFT) at the B3LYP/6–311 G(d,p) level is compared with the experimentally determined mol­ecular structure in the solid state.




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Crystal structure of 4,4'-(disulfanedi­yl)dipyridinium chloride triiodide

4,4'-(Disulfanedi­yl)dipyridinium chloride triiodide, C10H10N2S22+·Cl−·I3−, (1) was synthesized by reaction of 4,4'-di­pyridyl­disulfide with ICl in a 1:1 molar ratio in di­chloro­methane solution. The structural characterization of 1 by SC-XRD analysis was supported by elemental analysis, FT–IR, and FT–Raman spectroscopic measurements.




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Tri­fluoro­methane­sulfonate salt of 5,10,15,20-tetra­kis­(1-benzyl­pyridin-1-ium-4-yl)-21H,23H-porphyrin and its CaII complex

The synthesis, crystallization and characterization of a tri­fluoro­methane­sulfonate salt of 5,10,15,20-tetra­kis­(1-benzyl­pyridin-1-ium-4-yl)-21H,23H-por­phy­rin, C68H54N84+·4CF3SO3−·4H2O, 1·OTf, are reported in this work. The reaction between 5,10,15,20-tetra­kis­(pyridin-4-yl)-21H,23H-porphyrin and benzyl bromide in the presence of 0.1 equiv. of Ca(OH)2 in CH3CN under reflux with an N2 atmosphere and subsequent treatment with silver tri­fluoro­methane­sulfonate (AgOTf) salt produced a red–brown solution. This reaction mixture was filtered and the solvent was allowed to evaporate at room temperature for 3 d to give 1·OTf. Crystal structure determination by single-crystal X-ray diffraction (SCXD) revealed that 1·OTf crystallizes in the space group P21/c. The asymmetric unit contains half a porphyrin mol­ecule, two tri­fluoro­methane­sulfonate anions and two water mol­ecules of crystallization. The macrocycle of tetra­pyrrole moieties is planar and unexpectedly it has coordinated CaII ions in occupational disorder. This CaII ion has only 10% occupancy (C72H61.80Ca0.10F12N8O16S4). The pyridinium rings bonded to methyl­ene groups from porphyrin are located in two different arrangements in almost orthogonal positions between the plane formed by the porphyrin and the pyridinium rings. The crystal structure features cation⋯π inter­actions between the CaII atom and the π-system of the phenyl ring of neighboring mol­ecules. Both tri­fluoro­methane­sulfonate anions are found at the periphery of 1, forming hydrogen bonds with water mol­ecules.




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Structural characterization of the supra­molecular complex between a tetra­quinoxaline-based cavitand and benzo­nitrile

The structural characterization is reported of the supra­molecular complex between the tetra­quinoxaline-based cavitand 2,8,14,20-tetra­hexyl-6,10:12,16:18,22:24,4-O,O'-tetra­kis­(quinoxaline-2,3-di­yl)calix[4]resorcinarene (QxCav) with benzo­nitrile. The complex, of general formula C84H80N8O8·2C7H5N, crystallizes in the space group Poverline{1} with two independent mol­ecules in the asymmetric unit, displaying very similar geometrical parameters. For each complex, one of the benzo­nitrile mol­ecules is engulfed inside the cavity, while the other is located among the alkyl legs at the lower rim. The host and the guests mainly inter­act through weak C—H⋯π, C—H⋯N and dispersion inter­actions. These inter­actions help to consolidate the formation of supra­molecular chains running along the crystallographic b-axis direction.




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The crystal structures and Hirshfeld surface analysis of three new bromo-substituted 3-methyl-1-(phenyl­sulfon­yl)-1H-indole derivatives

Three new 1H-indole derivatives, namely, 2-(bromo­meth­yl)-3-methyl-1-(phenyl­sulfon­yl)-1H-indole, C16H14BrNO2S, (I), 2-[(E)-2-(2-bromo-5-meth­oxy­phen­yl)ethen­yl]-3-methyl-1-(phenyl­sulfon­yl)-1H-indole, C24H20BrNO3S, (II), and 2-[(E)-2-(2-bromo­phen­yl)ethen­yl]-3-methyl-1-(phenyl­sulfon­yl)-1H-indole, C23H18BrNO2S, (III), exhibit nearly orthogonal orientations of their indole ring systems and sulfonyl-bound phenyl rings. Such conformations are favourable for inter­molecular bonding involving sets of slipped π–π inter­actions between the indole systems and mutual C—H⋯π hydrogen bonds, with the generation of two-dimensional monoperiodic patterns. The latter are found in all three structures, in the form of supra­molecular columns with every pair of successive mol­ecules related by inversion. The crystal packing of the compounds is additionally stabilized by weaker slipped π–π inter­actions between the outer phenyl rings (in II and III) and by weak C—H⋯O, C—H⋯Br and C—H⋯π hydrogen bonds. The structural significance of the different kinds of inter­actions agree with the results of a Hirshfeld surface analysis and the calculated inter­action energies. In particular, the largest inter­action energies (up to −60.8 kJ mol−1) are associated with pairing of anti­parallel indole systems, while the energetics of weak hydrogen bonds and phenyl π–π inter­actions are comparable and account for 13–34 kJ mol−1.




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Crystal structures of four gold(I) complexes [AuL2]+[AuX2]− and a by-product (L·LH+)[AuBr2]− (L = substituted pyridine, X = Cl or Br)

Bis(2-methyl­pyridine)­gold(I) di­bromido­aurate(I), [Au(C6H7N)2][AuBr2], (1), crystallizes in space group C2/c with Z = 4. Both gold atoms lie on twofold axes and are connected by an aurophilic contact. A second aurophilic contact leads to infinite chains of alternating cations and anions parallel to the b axis, and the residues are further connected by a short H⋯Au contact and a borderline Br⋯Br contact. Bis(3-methyl­pyridine)­gold(I) di­bromido­aurate(I), [Au(C6H7N)2][AuBr2], (2), crystallizes in space group C2/m with Z = 2. Both gold atoms lie on special positions with symmetry 2/m and are connected by an aurophilic contact; all other atoms except for one methyl hydrogen lie in mirror planes. The extended structure is closely analogous to that of 1, although the structures are formally not isotypic. Bis(3,5-di­methyl­pyridine)­gold(I) di­chlor­ido­aurate(I), [Au(C7H9N)2][AuCl2], (3) crystallizes in space group Poverline{1} with Z = 2. The cation lies on a general position, and there are two independent anions in which the gold atoms lie on inversion centres. The cation and one anion associate via three short H⋯Cl contacts to form a ribbon structure parallel to the b axis; aurophilic contacts link adjacent ribbons. Bis(3,5-di­methyl­pyridine)­gold(I) di­bromido­aurate(I), [Au(C7H9N)2][AuBr2], (4) is isotypic to 3. Attempts to make similar compounds involving 2-bromo­pyridine led instead to 2-bromopyridinium di­bromido­aurate(I)–2-bromo­pyridine (1/1), (C5H5BrN)[AuBr2]·C5H4BrN, (5), which crystallizes in space group Poverline{1} with Z = 2; all atoms lie on general positions. The 2-bromo­pyridinium cation is linked to the 2-bromo­pyridine mol­ecule by an N—H⋯N hydrogen bond. Two formula units aggregate to form inversion-symmetric dimers involving Br⋯Br, Au⋯Br and H⋯Br contacts.




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Synthesis, spectroscopic analysis and crystal structure of (N-{2-[(2-amino­eth­yl)amino]­eth­yl}-4'-methyl-[1,1'-biphenyl]-4-sulfonamidato)tri­carb­on­ylrhenium(I)

The title compound, [Re(C17H22N3O2S)(CO)3] is a net neutral fac-Re(I)(CO)3 complex of the 4-methyl­biphenyl sulfonamide derivatized di­ethyl­enetri­amine ligand. The NNN-donor monoanionic ligand coordinates with the Re core in tridentate fashion, establishing an inner coordination sphere resulting in a net neutral complex. The complex possesses pseudo-octa­hedral geometry where one face of the octa­hedron is occupied by three carbonyl ligands and the other faces are occupied by one sp2 nitro­gen atom of the sulfonamide group and two sp3 nitro­gen atoms of the dien backbone. The Re—Nsp2 bond distance, 2.173 (4) Å, is shorter than the Re—Nsp3 bond distances, 2.217 (5) and 2.228 (6) Å, and is similar to the range reported for typical Re—Nsp2 bond lengths (2.14 to 2.18 Å).




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Crystal structure and Hirshfeld surface analysis of dimeth­yl(phen­yl)phosphine sulfide

The title compound, C8H11PS, which melts below room temperature, was crystallized at low temperature. The P—S bond length is 1.9623 (5) Å and the major contributors to the Hirshfeld surface are H⋯H (58.1%), S⋯H/H⋯S (13.4%) and C⋯H/H⋯C contacts (11.7%).




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Crystal structure determination and analyses of Hirshfeld surface, crystal voids, inter­molecular inter­action energies and energy frameworks of 1-benzyl-4-(methyl­sulfan­yl)-3a,7a-di­hydro-1H-pyrazolo­[3,4-d]pyrimidine

The pyrazolo­pyrimidine moiety in the title mol­ecule, C13H12N4S, is planar with the methyl­sulfanyl substituent lying essentially in the same plane. The benzyl group is rotated well out of this plane by 73.64 (6)°, giving the mol­ecule an approximate L shape. In the crystal, C—H⋯π(ring) inter­actions and C—H⋯S hydrogen bonds form tubes extending along the a axis. Furthermore, there are π–π inter­actions between parallel phenyl rings with centroid-to-centroid distances of 3.8418 (12) Å. A Hirshfeld surface analysis of the crystal structure indicates that the most important contributions to the crystal packing are from H⋯H (47.0%), H⋯N/N⋯H (17.6%) and H⋯C/C⋯H (17.0%) inter­actions. The volume of the crystal voids and the percentage of free space were calculated to be 76.45 Å3 and 6.39%, showing that there is no large cavity in the crystal packing. Evaluation of the electrostatic, dispersion and total energy frameworks indicate that the cohesion of the crystal structure is dominated by the dispersion energy contributions.




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Crystal structure of the 1:1 co-crystal 4-(di­methylamino)­pyridin-1-ium 8-hy­droxy­quinoline-5-sulfonate–N,N-di­methyl­pyridin-4-amine

The asymmetric unit of the title compound is composed of two independent ion pairs of 4-(di­methyl­amino)­pyridin-1-ium 8-hy­droxy­quinoline-5-sulfonate (HDMAP+·HqSA−, C7H11N2+·C9H6NO4S−) and neutral N,N-di­methyl­pyridin-4-amine mol­ecules (DMAP, C7H10N2), co-crystallized as a 1:1:1 HDMAP+:HqSA−:DMAP adduct in the monoclinic system, space group Pc. The compound has a layered structure, including cation layers of HDMAP+ with DMAP and anion layers of HqSA− in the crystal. In the cation layer, there are inter­molecular N—H⋯N hydrogen bonds between the protonated HDMAP+ mol­ecule and the neutral DMAP mol­ecule. In the anion layer, each HqSA− is surrounded by other six HqSA−, where the planar network structure is formed by inter­molecular O—H⋯O and C—H⋯O hydrogen bonds. The cation and anion layers are linked by inter­molecular C—H⋯O hydrogen bonds and C—H⋯π inter­actions.




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Crystal structure determination and Hirshfeld surface analysis of N-acetyl-N-3-meth­oxy­phenyl and N-(2,5-di­meth­oxy­phen­yl)-N-phenyl­sulfonyl derivatives of N-[1-(phenyl­sulfon­yl)-1H-indol-2-yl]methanamine

Two new [1-(phenyl­sulfon­yl)-1H-indol-2-yl]methanamine derivatives, namely, N-(3-meth­oxy­phen­yl)-N-{[1-(phenyl­sulfon­yl)-1H-indol-2-yl]meth­yl}acetamide, C24H22N2O4S, (I), and N-(2,5-di­meth­oxy­phen­yl)-N-{[1-(phenyl­sulfon­yl)-1H-indol-2-yl]meth­yl}benzene­sulfonamide, C29H26N2O6S2, (II), reveal a nearly orthogonal orientation of their indole ring systems and sulfonyl-bound phenyl rings. The sulfonyl moieties adopt the anti-periplanar conformation. For both compounds, the crystal packing is dominated by C—H⋯O bonding [C⋯O = 3.312 (4)–3.788 (8) Å], with the structure of II exhibiting a larger number, but weaker bonds of this type. Slipped π–π inter­actions of anti­parallel indole systems are specific for I, whereas the structure of II delivers two kinds of C—H⋯π inter­actions at both axial sides of the indole moiety. These findings agree with the results of Hirshfeld surface analysis. The primary contributions to the surface areas are associated with the contacts involving H atoms. Although II manifests a larger fraction of the O⋯H/H⋯O contacts (25.8 versus 22.4%), most of them are relatively distal and agree with the corresponding van der Waals separations.




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Crystal and mol­ecular structure of 2-methyl-1,4-phenyl­ene bis­(3,5-di­bromo­benzoate)

The aryl diester compound, 2-methyl-1,4-phenyl­ene bis­(3,5-di­bromo­benzoate), C21H12Br4O4, was synthesized by esterification of methyl hydro­quinone with 3,5-di­bromo­benzoic acid. A crystalline sample was obtained by cooling a sample of the melt (m.p. = 502 K/DSC) to room temperature. The mol­ecular structure consists of a central benzene ring with anti-3,5-di­bromo­benzoate groups symmetrically attached at the 1 and 4 positions and a methyl group attached at the 2 position of the central ring. In the crystal structure (space group Poverline{1}), mol­ecules of the title aryl diester are located on inversion centers imposing disorder of the methyl group and H atom across the central benzene ring. The crystal structure is consolidated by a network of C—H⋯Br hydrogen bonds in addition to weaker and offset π–π inter­actions involving the central benzene rings as well as the rings of the attached 3,5-di­bromo­benzoate groups.




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Synthesis, mol­ecular and crystal structures of 4-amino-3,5-di­fluoro­benzo­nitrile, ethyl 4-amino-3,5-di­fluoro­benzoate, and diethyl 4,4'-(diazene-1,2-di­yl)bis­(3,5-di­fluoro­benzoate)

The crystal structures of two inter­mediates, 4-amino-3,5-di­fluoro­benzo­nitrile, C7H4F2N2 (I), and ethyl 4-amino-3,5-di­fluoro­benzoate, C9H9F2NO2 (II), along with a visible-light-responsive azo­benzene derivative, diethyl 4,4'-(diazene-1,2-di­yl)bis­(3,5-di­fluoro­benzoate), C18H14F4N2O4 (III), obtained by four-step synthetic procedure, were studied using single-crystal X-ray diffraction. The mol­ecules of I and II demonstrate the quinoid character of phenyl rings accompanied by the distortion of bond angles related to the presence of fluorine substituents in the 3 and 5 (ortho) positions. In the crystals of I and II, the mol­ecules are connected by N—H⋯N, N—H⋯F and N—H⋯O hydrogen bonds, C—H⋯F short contacts, and π-stacking inter­actions. In crystal of III, only stacking inter­actions between the mol­ecules are found.




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Synthesis, mol­ecular and crystal structure of [(NH2)2CSSC(NH2)2]2[RuBr6]Br2·3H2O

The title compound, bis­[di­thio­bis­(formamidinium)] hexa­bromido­ruthenium dibromide trihydrate, [(NH2)2CSSC(NH2)2]2[RuBr6]Br2·3H2O, crystallizes in the ortho­rhom­bic system, space group Cmcm, Z = 4. The [RuBr6]2− anionic complex has an octa­hedral structure. The Ru—Br distances fall in the range 2.4779 (4)–2.4890 (4) Å. The S—S and C—S distances are 2.0282 (12) and 1.783 (2) Å, respectively. The H2O mol­ecules, Br− ions, and NH2 groups of the cation are linked by hydrogen bonds. The conformation of the cation is consolidated by intra­molecular O—H⋯Br, O—H⋯O, N—H⋯Br and N—H⋯O hydrogen bonds. The [(NH2)2CSSC(NH2)2]2+ cations form a hydrogen-bonded system involving the Br − ions and the water mol­ecules. Two Br − anions form four hydrogen bonds, each with the NH2 groups of two cations, thus linking the cations into a ring. The rings are connected by water mol­ecules, forming N—H⋯O—H⋯Br hydrogen bonds.




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Synthesis, crystal structure and Hirshfeld surface of ethyl 2-[2-(methyl­sulfan­yl)-5-oxo-4,4-diphenyl-4,5-di­hydro-1H-imidazol-1-yl]acetate (thio­phenytoin derivative)

The di­hydro­imidazole ring in the title mol­ecule, C20H20N2O3S, is slightly distorted and the lone pair on the tri-coordinate nitro­gen atom is involved in intra-ring π bonding. The methyl­sulfanyl substituent lies nearly in the plane of the five-membered ring while the ester substituent is rotated well out of that plane. In the crystal, C—H⋯O hydrogen bonds form inversion dimers, which are connected along the a- and c-axis directions by additional C—H⋯O hydrogen bonds, forming layers parallel to the ac plane. The major contributors to the Hirshfeld surface are C⋯H/H⋯C, O⋯H/H⋯O and S⋯H/H⋯S contacts at 20.5%, 14.7% and 4.9%, respectively.