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

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

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

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 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

The crystal structures of catena-poly[[μ-aqua-di-aqua-(μ3-2-methyl-propano-ato-κ4 O:O,O':O')calcium] 2-methyl-propano-ate dihydrate], {[Ca(C4H7O2)(H2O)3](C4H7O2)·2H2O} n , (I), catena-poly[[μ-aqua-di-aqua-(μ3-2-methyl-propano-ato-κ4 O:O,O':O')strontium] 2-methyl-propano-ate dihydrate], {[Sr(C4H7O2)(H2O)3](C4H7O2)·2H2O} n , (II), and catena-poly[[μ-aqua-di-aqua-(μ3-2-methyl-propano-ato-κ4 O:O,O':O')(calcium/strontium)] 2-methyl-propano-ate dihydrate], {[(Ca,Sr)(C4H7O2)(H2O)3](C4H7O2)·2H2O} n , (III), are related. (III) can be considered as an Sr-containing solid solution of (I), with Ca2+ and Sr2+ occupationally disordered in the ratio 0.7936 (16):0.2064 (16). (I)/(III) and (II) are homeotypic with different space groups of Pbca and Cmce, respectively. All the title crystal structures are composed of hydro-philic sheets containing the cations, carboxyl-ate groups as well as water mol-ecules. The hydro-phobic layers, which consist of 2-methyl-propano-ate chains, surround the hydro-philic sheets from both sides, thus forming a sandwich-like structure extending parallel to (001). The cohesion forces within these sheets are the cation-oxygen bonds and O-H⋯O hydrogen bonds of moderate strength. Stacking of these sandwiches along [001] is consolidated by van der Waals forces. The structures contain columns defined by the cation-oxygen inter-actions in which just one symmetry-independent 2-methyl-propano-ate anion is included, together with three water mol-ecules. These mol-ecules participate in an irregular coordination polyhedron composed of eight O atoms around the cation. Additional water mol-ecules as well as the second 2-methyl-propano-ate anion are not part of the coordination sphere. These mol-ecules are connected to the above-mentioned columns by O-H⋯O hydrogen bonds of moderate strength. In (II), the Sr2+ cation, two of the coordinating water mol-ecules and both anions are situated on a mirror plane with a concomitant positional disorder of the 2-methyl-propyl groups; the non-coordinating water mol-ecule also shows positional disorder of its hydrogen atom.

• Klíčová slova
• carboxyl­ates, hydrogen bonding, layered crystal structure, solid solution, the Cambridge Structural Database,
• 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 title alkali propano-ates poly[(μ5-propano-ato)alkali(I)], M +(C2H5COO)-, with alkali/M + = Na+, K+, Rb+ and Cs+, show close structural similarity, which is manifested by the coordination of the cations by six oxygen atoms in a chessboard motif, forming a bilayer. This bilayer is situated between hydro-phobic layers composed of dangling ethyl chains from the carboxyl-ate groups. Stacking of these two-dimensional sandwiches, which are parallel to (001), forms the title structures. Each metal cation is coordinated by six O atoms in the form of a distorted trigonal prism. One pair of these oxygen atoms belongs to a bridging, bidentately coordinating carboxyl-ate anion, while each of the other four oxygen atoms belongs to different carboxyl-ate groups, which are in a bridging monodentate mode. Despite the close similarity, each of the studied alkali propano-ates crystallizes in a different space group. The atoms are in general positions, except for the cation in K+(C2H5COO)-, which is situated on a mirror plane. Positional disorder of the methyl groups that are disordered over two positions is present in the Na+ and K+ propano-ates, in contrast to the Rb+ and Cs+ propano-ates. In the Na+ compound, the occupational parameters of the disordered methyl groups are different compared to the K+ compound where they are equal. This difference results in doubling of the a unit-cell parameter of the Na+ compound with respect to that of the K+ compound, otherwise the structures are homeotypic. In Cs+ propano-ate, a disorder of the methyl H atoms is observed.

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