The N-H...O hydrogen bond is the characteristic interaction in the crystal structures of N-benzyl-P-phenyl-N'-(p-tolyl)phosphonic diamide, C20H21N2OP or (C6H5)P(O)(NHCH2C6H5)(NHC6H4-p-CH3), (I), diphenylphosphinic 1-methylpropylamide, C16H20NOP or (C6H5)2P(O)[NHCH(CH3)(C2H5)], (II), (S)-1-phenylethylammonium N-[(S)-1-phenylethyl]phenylphosphonamidate, C8H12N+·C14H15NO2P- or [S-(C6H5)CH(CH3)NH3][(C6H5)P(O){S-NHCH(CH3)(C6H5)}(O)], (III), and (4-methylbenzyl)ammonium diphenylphosphinate, C8H12N+·C12H10O2P- or [4-CH3-C6H4CH2NH3][(C6H5)2P(O)(O)], (IV). This article focuses on the N-H...O hydrogen bonds by considering the structures of (I), (II), (III) and (IV), and reviewing their analogous compounds, including 43 (C)P(O)(N)2, 102 (C)2P(O)(N), 31 (C)P(O)(N)(O) and 96 (C)2P(O)(O) structures, deposited in the Cambridge Structural Database (CSD). For the structures with a (C)P(O)(N)2 segment, only neutral hydrogen bonds were found in the CSD. The other three classes of compounds included both neutral and `charge-assisted' hydrogen bonds, and the (C)2P(O)(O) structures were particularly noticeable for a high number of cation-anion compounds. The overall tendencies of N...O distances in neutral and cation-anion compounds were compared. The N-H...O hydrogen-bond angles were also analyzed for the four classes of phosphorus compounds.

• Klíčová slova
• Cambridge Structural Database, crystal structure, hydrogen bonding, phosphorus compound, positive/negative charge-assisted N—H...O hydrogen bonds,
• Publikační typ
• časopisecké články MeSH

For [C(O)NH](N)2P(O)-based structures, the magnitude of the differences in the N-H...O, H...O=P and H...O=C angles has been evaluated when the N-H bond lengths, determined by X-ray diffraction, were compared to the neutron normalized values and the maximum percentage difference was obtained, i.e. about 3% for the angle even if the N-H bond lengths have a difference of about 30% (0.7 Å for the X-ray and 1.03 Å for the neutron-normalized value). The symmetries of the crystals are discussed with respect to the symmetry of the molecules, as well as to the symmetry of hydrogen-bonded motifs, and the role of the most directional hydrogen bond in raising the probability of obtaining centrosymmetric crystal structures is investigated. The work was performed by considering nine new X-ray crystal structures and 204 analogous structures retrieved from the Cambridge Structural Database.

• Klíčová slova
• Cambridge Structural Database, X-ray diffraction, lone electron pair, neutron normalization, phosphoric triamide, symmetry,
• Publikační typ
• časopisecké články MeSH

The crystal structures of diphenyl (cycloheptylamido)phosphate, C19H24NO3P or (C6H5O)2P(O)(NHC7H13), (I), and diphenyl (dibenzylamido)phosphate, C26H24NO3P or (C6H5O)2P(O)[N(CH2C6H5)2], (II), are reported. The NHC7H13 group in (I) provides two significant hydrogen-donor sites in N-H...O and C-H...O hydrogen bonds, needed for a one-dimensional hydrogen-bond pattern along [100] in the crystal, while (II), with a (C6H5CH2)2N moiety, lacks these hydrogen bonds, but its three-dimensional supramolecular structure is mediated by C-H...π interactions. The conformational behaviour of the phenyl rings in (I), (II) and analogous structures from the Cambridge Structural Database (CSD) were studied in terms of flexibility, volume of the other group attached to phosphorus and packing forces. From this study, synclinal (±sc), anticlinal (±ac) and antiperiplanar (±ap) conformations were found to occur. In the structure of (II), there is an intramolecular Cortho-H...O interaction that imposes a +sc conformation for the phenyl ring involved. For the structures from the CSD, the +sc and ±ap conformations appear to be mainly imposed by similar Cortho-H...O intramolecular interactions. The large contribution of the C...H/H...C contacts (32.3%) in the two-dimensional fingerprint plots of (II) is a result of the C-H...π interactions. The differential scanning calorimetry (DSC) analyses exhibit peak temperatures (Tm) at 109 and 81 °C for (I) and (II), respectively, which agree with the strengths of the intermolecular contacts and the melting points.

• Klíčová slova
• Cambridge Structural Database, amidophosphoester, conformational flexibility, crystal structure, energy framework, hydrogen bonding,
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH

A seventh blind test of crystal structure prediction has been organized by the Cambridge Crystallographic Data Centre. The results are presented in two parts, with this second part focusing on methods for ranking crystal structures in order of stability. The exercise involved standardized sets of structures seeded from a range of structure generation methods. Participants from 22 groups applied several periodic DFT-D methods, machine learned potentials, force fields derived from empirical data or quantum chemical calculations, and various combinations of the above. In addition, one non-energy-based scoring function was used. Results showed that periodic DFT-D methods overall agreed with experimental data within expected error margins, while one machine learned model, applying system-specific AIMnet potentials, agreed with experiment in many cases demonstrating promise as an efficient alternative to DFT-based methods. For target XXXII, a consensus was reached across periodic DFT methods, with consistently high predicted energies of experimental forms relative to the global minimum (above 4 kJ mol-1 at both low and ambient temperatures) suggesting a more stable polymorph is likely not yet observed. The calculation of free energies at ambient temperatures offered improvement of predictions only in some cases (for targets XXVII and XXXI). Several avenues for future research have been suggested, highlighting the need for greater efficiency considering the vast amounts of resources utilized in many cases.

• Klíčová slova
• Cambridge Structural Database, blind test, crystal structure prediction, lattice energy, polymorphism,
• Publikační typ
• časopisecké články MeSH

The conformational flexibilities are studied in two new organotin(IV) complexes, namely, trans-dichloridodimethylbis[N,N',N''-tris(2-chlorobenzyl)phosphoric triamide]tin(IV), [Sn(CH3)2(C21H21Cl3N3OP)2Cl2] or Sn(CH3)2Cl2{OP[NHCH2C6H4(2-Cl)]3}2, (I), and bis(dipropylammonium) tetrachloridodimethylstannate(IV), [(CH3CH2CH2)2NH2]2[Sn(CH3)2Cl4], (II), and their analogous structures from the Cambridge Structural Database (CSD). The conformations are considered based on the N-P=O-Sn torsion angles for (I) and the C-C-C-N, C-C-N-C, C-N-C-C and N-C-C-C torsion angles for the two symmetry-independent [CH3CH2CH2NH2CH2CH2CH3]+ cations in (II), and the ±ac±sp±ac (ac = anticlinal and sp = synperiplanar) and ±ap±ap±ap±ap (ap = antiperiplanar) conformations are observed, respectively. In both structures, the four atoms in the corners of the square-planar segment of the octahedral shape around the Sn atom participate in normal hydrogen-bonding interactions as acceptors, which include two O and two Cl atoms for (I), and four Cl atoms for (II). However, the phosphoric triamide ligands block the environment around the Sn atom and limit the hydrogen-bond pattern to form a supramolecular ribbon assembly, while in the presence of small organic cations in (II), a two-dimensional hydrogen-bonded architecture is achieved. The weak interactions π-π, C-H...π and C-Cl...π in (I), and C-H...Cl in (II) do not change the dimensionality of the hydrogen-bond pattern. The 62 CSD structures analogous to (I), i.e. with an SnOPN3 segment (including 83 entries) fall into four categories of conformations based on the N-P=O-Sn torsion angles. The 132 [(CH3CH2CH2)2NH2]+ cations from 85 CSD structures are classified into seven groups based on the torsion angles noted for (II). Most of the CSD structures adopt the same associated conformations noted for (I) and (II). 15 [Sn(CH3)2Cl4]2- anions extracted from the CSD are compared with the structure of (II).

• Klíčová slova
• Cambridge Structural Database, Hirshfeld surface analysis, conformational analysis, crystal structure, organotin(IV) complex, phosphoric triamide,
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH

Orthophthalaldehyde (o-phthalaldehyde, OPA) is an aromatic dialdehyde bearing two electron-withdrawing carbonyl groups. The reactions of OPA with primary amines are broadly applied for the synthesis of important heterocyclic compounds with biological relevance. A number of such reactions have been investigated recently and several structures of condensation products have been reported, however, the complex reaction mechanism is still not fully understood and comprises concurrent as well as consecutive reactions. The reaction products depend on the primary amine which reacts with OPA, the reaction environment (solvent) and the proportion of the reactants. The title molecule, C11H13NO, the product of the reaction of OPA with isopropylamine, contains a five-membered pyrrole C4N ring with a carbonyl substituent, which forms part of the isoindolinone unit. Though this pyrrole ring contains one C atom in the sp(3)-hybridized state, it is fairly planar. The title molecule has been compared with similar structures retrieved from the Cambridge Structural Database in order to study this phenomenon. The planarity of this fragment has been explained by the presence of partially delocalized C-C, C-N and C-O bonds, and by an inner angle in the planar pentagonal ring (∼108°), which is close to the ideal tetrahedral value for the sp(3)-hybridized state of the constituent C atom. Due to this propitious angle, this C atom can be present in states intermediate between sp(3)- and sp(2)-hybridized in different structures, while still maintaining the planarity of the ring. There are only weak intermolecular C-H...O hydrogen bonds and C-H...π-electron ring interactions in the structure. In particular, it is the pyrrole ring which is involved in these interactions.

• Klíčová slova
• Cambridge Structural Database, angle strain, aromaticity, crystal structure, heterocyclic compounds, isoindolinone, isoindolone, orthophthalaldehyde, planarity, reaction mechanism,
• Publikační typ
• časopisecké články MeSH

The structure of the title compound, [K2(C4H7O2)2(H2O)] n , is composed of stacked sandwiches, which are formed by cation-oxygen bilayers surrounded by methyl-ethyl hydro-phobic chains. These sandwiches are held together by van der Waals inter-actions between the methyl-ethyl groups. The methyl-ethyl groups are disordered over two positions with occupancies 0.801 (3):0.199 (3). The potassium cations are coordinated by seven O atoms, which form an irregular polyhedron. There is a water mol-ecule, the oxygen atom of which is situated in a special position on a twofold axis (Wyckoff position 4e). The water H atoms are involved in Owater-H⋯Ocarbox-yl hydrogen bonds of moderate strength. These hydrogen bonds are situated within the cation-oxygen, i.e. hydro-philic, bilayer.

• Klíčová slova
• Cambridge Structural Database, crystal structure, metal–organic framework compounds, methyl­propano­ate,
• Publikační typ
• časopisecké články MeSH

The crystal structures of two single-enantiomer amidophosphoesters with an (O)2P(O)(N) skeleton, i.e. diphenyl [(R)-(+)-α-methylbenzylamido]phosphate, (I), and diphenyl [(S)-(-)-α-methylbenzylamido]phosphate, (II), both C20H20NO3P, are reported. In both structures, chiral one-dimensional hydrogen-bonded architectures, along [010], are mediated by N-H...OP interactions. The statistically identical assemblies include the noncentrosymmetric graph-set motif C(4) and the compounds crystallize in the chiral space group P21. As a result of synergistic co-operation from C-H...O interactions, a two-dimensional superstructure is built including a noncentrosymmetric R44(22) hydrogen-bonded motif. A Cambridge Structural Database survey was performed on (O)2P(O)(N)-based structures in order to review the frequency of space groups observed in this family of compounds; the hydrogen-bond motifs in structures with chiral space groups and the types of groups inducing chirality are discussed. The 2,3JX-P (X = H or C) coupling constants from the NMR spectra of (I) and (II) have been studied. In each compound, the two diastereotopic C6H5O groups are different, which is reflected in the different chemical shifts and some coupling constants.

• Klíčová slova
• NMR, amidophosphoester, crystal structure, diastereotopic, hydrogen bonding, phosphate, single enantiomer,
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH

The crystal structure of the title complex, [Pb3(C4H7O2)6(H2O)2] n , was redetermined on basis of modern CCD-based single-crystal X-ray data at 120 K. The current study basically confirms the previous report [Fallon et al. (1997 ▸). Polyhedron, 16, 19-23] at 190 K, but with higher accuracy and precision. In particular, positional disorder of one of the 2-methyl-propano-ate anions over two sets of sites was resolved, showing a refined ratio of the disorder components of 0.535 (9):0.465 (9). The three independent cations in the structure have coordination numbers of [7 + 1], [6 + 1], and [5 + 3], with O atoms belonging either to carboxyl-ate groups or water mol-ecules. This arrangement leads to the formation of sheets parallel to (01), whereby the hydro-phobic 2-methyl-propanyl groups of the anions are oriented above and below the hydro-philic sheets to form a layered structure. Within a sheet, hydrogen bonds of the type Owater-H⋯O are formed, whereas the hydro-phobic groups between adjacent layers inter-act through van der Waals forces.

• Klíčová slova
• carboxyl­ates, crystal structure, hydrogen bonding, the Cambridge Structural Database,
• Publikační typ
• časopisecké články MeSH

This study investigates venetoclax solvates and their nonsolvated forms through desolvation. Seven solvates were prepared and their structures solved from single-crystal X-ray diffraction data. Among these, two are cavity solvates while the remaining five are channel solvates, with three being isomorphous. Desolvation experiments led to two solvent-free crystalline polymorphs of venetoclax, forms A and B. Notably, the acetone solvate remained stable and did not convert to a nonsolvated form. Form B has a higher melting point and a faster intrinsic dissolution rate than form A. Advanced computational tools, including Solvate Analyser and CSD-Particle, provided insights into crystal surface properties and desolvation behaviour. Properties such as lattice energy, molecular interaction energy, attachment energy, surface rugosity and solvent arrangement within the crystal and on the surface were linked to solvate stability and subsequent transformation upon desolvation. A combination of FTIR, and 13C and 15N solid-state NMR spectroscopies showed that both short- and long-range molecular interactions and arrangements of venetoclax molecules in the desolvated forms closely resembled those in the parent solvates.

• Klíčová slova
• Cambridge Structural Database, crystal engineering, crystal morphology, crystal structures, desolvation, intermolecular interactions, pharmaceuticals, polymorphism, solvates, venetoclax,
• Publikační typ
• časopisecké články MeSH