Sum Of Bond Angles Research Articles

3d-metal macrocyclic complexes containing porphyrazine/ perfluoroporphyrazine and fluoro ligands: Structural and thermodynamic parameters according to the various DFT model chemistries

By using three independent of density functional theory (DFT) model chemistries with functionals B3PW91, M06 and OPBE, and the TZVP basis set, combining the D3 version of Grimme’s dispersion with the original D3 damping function, the molecular structures of three types of 3[Formula: see text] element (M) macrocyclic coordination compounds — homoligand with porphyrazine (H2L1), heteroligand with porphyrazine and two axially oriented fluoro ligands and heteroligand with perfluoroporphyrazine (H2L2) and two axially oriented fluoro ligands having [ML1], [ML1(F)2] and [ML2(F)2] compositions, respectively, were calculated. The values of the most important bond lengths, bond and non-bond angles in the resulting metal complexes, and NBO analysis data are presented. It was noted that almost each of these complexes contains a coplanar MN4 chelate unit and a group of N4 atoms, as well as coplanar 5- and 6-membered rings; moreover, both of them are pairwise identical to each other in terms of the sums of bond angles (540[Formula: see text] and 720[Formula: see text], respectively) and their assortments. Bond angles formed by M atoms and two fluorine atoms are 180[Formula: see text]; bond angles formed by fluorine, M and nitrogen atoms are 90[Formula: see text]. NBO analysis of all the above 3[Formula: see text]-metal chelates was carried out, and based on the data, a high degree of delocalization of the electron density in these coordination compounds was stated. The values of the standard enthalpy [Formula: see text], entropy [Formula: see text] and Gibbs energy [Formula: see text] of formation of these compounds were also calculated. Particular attention was paid to the fact that according to these data, for the ([ML1]) and ([ML1(F)2]) complexes the values of [Formula: see text] and [Formula: see text] are positive, whereas for ([ML2(F)2]) complexes they are negative, and in the series [ML1] – [ML1(F)2] – [ML2(F)2] there is an increase in the thermodynamic stability of the complexes, which is undoubtedly due to the presence of peripheral fluorine substituents in the [ML2(F)2] structure. There was also good agreement between similar parameters calculated by different DFT methods, both qualitatively and quantitatively.

1-(Phenyl-sulfon-yl)-1H-indole-2-carbaldehyde.

The title compound, C15H11NO3S, was prepared by a facile synthetic approach. The N atom in the pyrrole ring of the indole moiety is pyramidal (bond-angle sum = 350.0°) and the phenyl ring of the phenyl-sulfonyl motif forms a dihedral angle of 76.24 (7)° with the mean plane of the indole ring system. In the crystal, C-H⋯O and C-H⋯π inter-actions link the mol-ecules into a three-dimensional network.

(E)-Benzyl 2-{4-[eth-yl(2-hy-droxy-eth-yl)amino]-benzyl-idene}hydrazinecarbodi-thio-ate.

In the title compound, C19H23N3OS2, the dihedral angle between the aromatic rings is 86.80 (8)° and the tertiary amine grouping is almost planar (bond-angle sum at the N atom = 360.0°). In the crystal, pairwise N-H⋯O hydrogen bonds link the mol-ecules into inversion dimers, and O-H⋯S hydrogen bonds link the dimers into [101] chains.

N,N'-Di-cyclo-hexyl-N-(phthaloylglyc-yl)urea.

The mol-ecular structure of the title compound {systematic name: 1,3-di-cyclo-hexyl-1-[2-(1,3-dioxo-2,3-di-hydro-1H-isoindol-2-yl)acet-yl]urea}, C23H29N3O4, derived from N,N'-di-cyclo-hexyl-urea, shows that the tertiary N atom substituted by a cyclo-hexyl and phthaloylglycyl groups adopts a perfectly planar geometry (bond-angle sum = 360.0°). In the same way as for N,N'-di-cyclo-hexyl-urea, the extended structure of the title compound features N-H⋯O hydrogen bonds, which generate chains of mol-ecules running in the [001] direction.

О взаимодействии азина циклогексанона с PBr3. Кристаллическая структура трис(4-бром-3a,6a-диаза-1,4-дифосфапентален-1-ил)амина

The interaction of cyclohexanone azine with phosphorus(III) bromide without a solvent has been studied. It has been shown that the main reaction product is cyclohexane-annelated 1,4-dibromo-3а,6а-diaza-1,4-diphosphapentalene (2, DDP-Br2, 57 %). The by-products of the synthesis are tris(4-bromo-3а,6а-diaza-1,4-diphosphapentalen-1-yl)amine (3, 8 %) and ammonium bromide. The molecular structure of compound 3 has been studied by X-ray analysis. The crystal cell contains two pairs of enantiomers and eight THF solvate molecules, four of which are disordered over two positions. The central nitrogen atom N(7) in compound 3 forms three bonds with the phosphorus atoms of the DDP fragments P(1), P(3), P(5), located in the same plane. The nitrogen atoms of the heteropentalene fragments (N(2), N(4), N(6)) that are located closer to the center of the molecule have a planar configuration (with the sum of bond angles 359.62, 359.50, 359.38°, respectively). In its turn, for the N(1), N(3), N(5) atoms, a greater deviation from the planar structure is observed (the sum of bond angles is 353.85, 353.71, 353.96°, respectively). The peripheral phosphorus-nitrogen bonds (P(2)-N(1) 1.689(2), P(4)-N(3) 1.691(3), P(6)-N(5) 1.690(2) Å) are shorter than the corresponding bonds in neighboring five-membered rings (P(1)-N(2) 1.744(2), P(3)-N(4) 1.738(3), P(5)-N(6) 1.733(2) Å). The difference in the phosphorus-bromine bond lengths P(2)-Br(1) 2.4805(8), P(4)-Br(2) 2.4675(8), and P(6)-Br(3) 2.4836(8) Å can be caused by the presence of various short contacts Br•••H between the adjacent molecules of compound 3, as well as between compound 3 and the THF solvate molecules. It is assumed that compound 3 is formed during the side reaction of DDP dibromide (2) with ammonium bromide, which appeared in the reaction mixture as a result of the partial decomposition of cyclohexanone azine upon prolonged heating with phosphorus bromide.

Ethyl 3,4-bis-(acet-yloxy)-2-(4-meth-oxy-phen-yl)pyrrol-idine-1-carboxyl-ate.

The title pyrrolidine compound, C18H23NO7, is a tetra-substituted species in which the five-membered ring has a twisted conformation with the twist occurring in the C-C bond bearing the adjacent acet-yloxy substituents; the Cm-Ca-Ca-Cp torsion angle is -40.76 (18)° [m = methyl-ene, a = acet-yloxy and p = phen-yl]. The N atom, which is sp 2-hybridized [sum of bond angles = 359.4°], bears an ethyl-carboxyl-ate substitutent and is connected to a methyl-ene-C atom on one side and a carbon atom bearing a 4-meth-oxy-phenyl group on the other side. Minor disorder is noted in the ethyl-carboxyl-ate substituent as well as in one of the acet-yloxy groups; the major components of the disorder have site occupancies of 0.729 (9) and 0.62 (3), respectively. The most notable feature of the mol-ecular packing is the formation of helical, supra-molecular chains aligned along the b-axis direction whereby the carbonyl-O atom not involved in a disordered residue accepts C-H⋯O inter-actions from methyl-ene-H and two-C atom separated methine-H atoms to form a six-membered {⋯HCCCH⋯O} synthon.

DFT Quantum-Chemical Calculations of Molecular Structures for Heteroligand M(III) Complexes of 3d Elements with Porphyrazine and Fluoride Ion

The molecular structures of heteroligand (6666)macrotetracyclic chelates of M(III) (M = Sc, Ti, V, Cr, Mn, Fe, Co, Ni, or Cu) with porphyrazine (an (NNNN)-donating ligand) and F– ion are calculated by the DFT OPBE/TZVP method. The key bond lengths, bond angles, and nonbonded angles in these complexes are reported. The standard enthalpies, entropies, and Gibbs free energies of formation are calculated for the complexes. All complexes have a slightly distorted tetragonal-pyramidal geometry, where the complex former M(III) is to some degree raised above the pyramid base made up of the donor nitrogen atoms. Characteristically, all 6-membered metal chelate rings in these metal chelates are identical to one another both in terms of the sum of bond angles and in their varieties.

Crystal structures and quantum chemical calculations of dichloro[4-(dimethylamino)phenyl]arsine and tris[4-(dimethylamino)phenyl]arsine

Dichloro[4-(dimethylamino)phenyl]arsine (1) and tris[4-(dimethylamino)phenyl]arsine (2) were synthesized and characterized using single crystal X-ray diffraction studies, NMR spectroscopy, IR spectroscopy and elemental analyses techniques. The X-ray structure analysis of 1 (P1¯, triclinic, Z = 4; R1 = 0.0478) revealed two crystallographically independent molecules in the asymmetric part of the unit cell. The average AsCl bond (220.6 p.m.) is found to be slightly longer than that of arsenic(III) chloride (216.1 or 216.2 p.m.), but to be rather similar to that in the orthorhombic modification of chlorobis[2,4,6-tris(trifluoromethyl)phenyl]arsine (219.2 p.m.). Mean As–Caryl (191.7 p.m.) and Caryl–N bond lengths (135.9 p.m.) suggest extended electronic interactions between the dichloroarsanyl group, the π-electron system of the arene ring and the nitrogen lone pair. In both molecules the nitrogen atoms are found in a planar coordination sphere; the sums of bond angles vary only slightly between 359.1° for 1a and 359.9° for 1b. In contrast to these observations, sums of bond angles of 292.7° for 1a and 293.98° for 1b indicate a pyramidal coordination sphere at arsenic. As well, the X-ray structure analysis of 2 (P1¯, triclinic, Z = 2; R1 = 0.0347) reveals bond lengths and angles at arsenic (AsC 194.9 p.m., CAsC 99.3°, AsCC 121.3°) as to be expected and obtained for similar compounds such as triphenyl arsine or triphenyl arsine derivatives. The sums of angles at two of the nitrogen atoms amount to values of 353.6° and 356.1° and deviate significantly from the value of the third (348.1°). Hence, two of three dimethylamino groups are found to be almost planar, whereas the third group shows a coordination sphere which has to be classified as an intermediate between trigonal planar and trigonal pyramidal. The molecule shows a high degree of C3 pseudosymmetry; the sum of angles at arsenic amounts to 298.0°. The average Caryl–N bond length (139.0 p.m.) suggests an interaction of the nitrogen lone pair with the π-system of the arene ring but it turns out to be much weaker than in dichloro[4-(dimethylamino)phenyl]arsine (1). Additionally, quantum chemical calculations were performed on several para substituted dichlorophenyl arsine compounds in order to ascertain optimized structural data and to shed some light onto these phenomena. Indeed, the aforementioned shortening of the N–Cipso bond to 135.9 p.m. can only in part be attributed to the well-known electronic interaction between the lone pair at nitrogen and the antibonding π∗ orbitals of the adjacent Cipso–Cortho bonds – on an average, these two distances are significantly elongated by 1.7 p.m. with respect to the standard value (140 p.m.).

Crystal structures of the two epimers from the unusual thermal C6-epimerization of 5-oxo-1,2,3,5,5a,6,7,9b-octa-hydro-7,9a-ep-oxy-pyrrolo-[2,1-a]iso-indole-6-carb-oxy-lic acid, 5a(RS),6(SR),7(RS),9a(SR),9b(SR) and 5a(RS),6(RS),7(RS),9a(SR),9b(SR).

The isomeric title compounds, C12H13NO4 (Ia) and C12H13NO4 (IIa), the products of an usual thermal C6-epimerization of 5-oxo-1,2,3,5,5a,6,7,9b-octa-hydro-7,9a-ep-oxy-pyrrolo-[2,1-a]iso-indole-6-carb-oxy-lic acid, represent the two different diastereomers and have very similar mol-ecular geometries. The mol-ecules of both compounds comprise a fused tetra-cyclic system containing four five-membered rings (pyrrolidine, pyrrolidinone, di-hydro-furan and tetra-hydro-furan), all of which adopt the usual envelope conformations. The dihedral angle between the basal planes of the pyrrolidine and pyrrolidinone rings are 14.3 (2) and 16.50 (11)°, respectively, for (Ia) and (IIa). The nitro-gen atom has a slightly pyramidalized geometry [bond-angle sum = 355.9 and 355.3°, for (Ia) and (IIa)], respectively. In the crystal of (Ia), mol-ecules form zigzag-like hydrogen-bonded chains along [010] through strong O-H⋯O hydrogen bonds and are further linked by weak C-H⋯O hydrogen bonds into complex two-tier layers parallel to (100). Unlike (Ia), the crystal of (IIa) contains centrosymmetric cyclic hydrogen-bonded dimers [graph set R22(14)], formed through strong O-H⋯O hydrogen bonds and are further linked by weak C-H⋯O hydrogen bonds into ribbons extending across [101].

(5,7-Dimethyl-2-oxo-2H-chromen-4-yl)methyl morpholine-4-carbodithioate

In the title compound, C17H19NO3S2, the 2H-chromene ring system is nearly planar, with a maximum deviation of 0.080 (2) Å, and the morpholine ring adopts a chair conformation. The bond-angle sum at the N atom is 358°. The coumarin unit makes dihedral angle of 86.34 (9)° with the morpholine ring. A short intramolecular C—H...S contact generates anS(7) ring. In the crystal, inversion dimers linked by pairs of weak C—H...O hydrogen bonds generateR22(16) loops. Aromatic π–π interactions interactions [shortest centroid–centroid distance = 3.8599 (13) Å] also occur.

Ethyl 2-(5-bromo-2-iodoanilino)cyclopent-1-ene-1-carboxylate

In the title compound, C14H15BrINO2, the conformation of the C—O—CH2—CH3grouping isanti[torsion angle = 173.8 (6)°] and the bond-angle sum at the N atom bridging the two rings is 360°. An unusual intramolecular bifurcated N—H...(O,I) hydrogen bond helps to establish the molecular conformation, in which the I atom and the C=O grouping aresyn. In the crystal, inversion dimers created by pairs of short intermolecular C—I...O interactions [C—I = 2.080 (7) Å; I...O = 3.211 (5) Å; C—I...O = 152.4 (2)°] occur.

Crystal structure of (E)-3-[4-(benzylideneamino)-5-sulfanylidene-3-(p-tolyl)-4,5-dihydro-1H-1,2,4-triazol-1-yl]-3-(4-methoxyphenyl)-1-phenylpropan-1-one

The title compound, C32H28N4O2S, crystallizes as a racemate. In the mol­ecule, the bond-angle sum at the C atom of the sulfanyl­idene entity bound to the triazole ring is 360°, with an annular N—C—N bond angle of 102.6 (2)° and two larger N—C—S angles of 127.3 (2) and 130.1 (2)°. The essentially planar 1,2,4-triazole ring (r.m.s. deviation = 0.013 Å) is nearly perpendicular to the phenylpropanone and methoxyphenyl rings , making dihedral angles of 76.9 (2) and 85.2 (2)°, respectively and subtends dihedral angles of 17.6 (2) and 40.3 (2)° with the tolyl and benzylideneamino rings, respectively. There is no π–π stacking between the mol­ecules. The crystal packing is dominated by weak C—H⋯O and C—H⋯N inter­actions, leading to a three-dimensional network structure. An intra­molecular C—H⋯S inter­action also occurs.

Crystal structure of 4-methyl-N-{(E)-meth-yl[(3aR,8aS)-2-oxo-3,3a,8,8a-tetra-hydro-2H-indeno-[1,2-d][1,3]oxazol-3-yl]-λ(4)-sulfanyl-idene}benzene-sulfonamide.

The formulation that the title compound, C18H18N2O4S2, adopts is a zwitterionic core with the charge separated to the sulfilimine S and N atoms and is supported by the two different S—N bond distances about the sulfinimine N atom [1.594 (2) and 1.631 (2) Å, respectively] that are typical for such bonds. The notably unusual bond is S—N(oxazolidinone) [1.692 (2) Å] that is longer than a typical S—N bond [1.603 (18) Å, Mogul analysis; Macrae et al. (2008 ▸). J. Appl. Cryst. 41, 466–470]. The bond-angle sum about sulfilimine sulfur (308.35°) reflects the trigonal–pyramidal geometry of this atom. Two of the angles are less than 100°. Despite the pyramidalization of this sulfur, there are no significant inter­molecular inter­actions, beyond usual van der Waals contacts, in the crystal packing.

Crystal structure of (4-hy-droxy-piperidin-1-yl)(4-methyl-phen-yl)methanone.

In the title compound, C13H17NO2, the dihedral angle between the planes of the piperidine and benzene rings is 51.7 (2)°. The bond-angle sum around the N atom [359.8 (3)°] indicates sp 2 hybridization of the atom. In the crystal, O—H⋯O hydrogen bonds link the mol­ecules, forming chains along [001].

Crystal structure of (4-hy-droxy-piperidin-1-yl)[4-(tri-fluoro-meth-yl)phen-yl]methanone.

The title compound, C13H14NO2F3, crystallises with two mol­ecules, A and B, in the asymmetric unit, with similar conformations. The dihedral angles between the piperidine and phenyl rings are 83.76 (2) and 75.23 (2)° in mol­ecules A and B, respectively. The bond-angle sums around the N atoms [359.1 and 359.7° for mol­ecules A and B, respectively] indicate sp 2 hybridization for these atoms. In the crystal, O—H⋯O hydrogen bonds link the mol­ecules into separate [100] chains of A and B mol­ecules. The chains are cross-linked by C—H⋯O inter­actions, generating alternating (001) sheets of A and B mol­ecules.

Crystal structure of 2-methyl-sulfanyl-1-(thio-morpholin-4-yl)-ethanone.

In the title compound, C7H13NOS2, the thio­morpholine ring adopts a chair conformation and the bond-angle sum at the N atom is 360°. The dihedral angle between the amide group and the thio­morpholine ring (all atoms) is 36.48 (12)°. In the crystal, C—H⋯O and C—H⋯S hydrogen bonds link adjacent mol­ecules, forming two-dimensional networks extending parellel to the (011) plane.

Crystal structure of 1-[(6-chloro-pyridin-3-yl)sulfon-yl]-1,2,3,4-tetra-hydro-quinoline.

The tetra-hydro-pyridine ring of the quinoline system in the title compound, C14H13ClN2O2S, adopts a half-chair conformation with the bond-angle sum at the N atom being 350.0°. The dihedral angle between the least-squares planes of the two aromatic rings is 50.13 (11)°. In the crystal, inversion dimers linked by pairs of C-H⋯O hydrogen bonds generate R 2 (2)(10) loops. Additional inter-molecular C-H⋯O hydrogen bonds generate C(7) chains along [100].

A new phosphorothioic triamide structure: P(S)[NHCH₂C₆H₅]₃.

The structure of N,N',N''-tribenzylphosphorothioic triamide, C21H24N3PS, (I), and analysis of the bond-angle sums at the N atoms for this compound, and for 74 structures with a P(S)[N]3 skeleton and the N atom in a three-coordinate geometry found in the Cambridge Structural Database [CSD; Groom & Allen (2014). Angew. Chem. Int. Ed. 53, 662-671], are reported. For (I), the bond-angle sum at one of the N atoms [359 (1)°] shows a nearly planar configuration, while the other two show a nonplanar geometry with bond-angle sums of 342 (1) and 347 (1)°. The location of the atoms attached to the nonplanar N atoms suggests an anti orientation of the corresponding lone electron pairs (LEPs) on these N atoms with respect to the P=S group. For 74 structures with a P(S)[N]3 skeleton and with the N atom in a three-coordinate geometry, the bond-angle sums at the N atoms were found to be in the range 293-360°. Among 307 such three-coordinate N atoms, 39% (120 N atoms) have bond-angle sums in the range 359-360°, in accordance with sp(2) hybridization, and 45% (138 N atoms) have bond-angle sums in the range 352-359°, with hybridization close to sp(2). For the orientation of the LEP with respect to the P=S group, the anti orientation was found to be a general rule for N atoms, with the corresponding bond-angle sums deviating by more than 8° from the planar value of 360°. In the title structure, the S atom takes part in intermolecular (N-H···)(N-H···)S hydrogen bonds, connecting the molecules into extended chains parallel to the b axis. The co-operation of one N atom in an N-H···S hydrogen bond as an H-atom donor, and in an N-H···N hydrogen bond as an acceptor, is a novel feature of the crystal structure.

Crystal structure of 1-benzyl-sulfonyl-1,2,3,4-tetra-hydro-quinoline.

In the title compound, C16H17NO2S, the heterocyclic ring adopts a half-chair conformation and the bond-angle sum at the N atom is 354.6°. The dihedral angle between the planes of the aromatic rings is 74.15 (10)°. In the crystal, mol­ecules are linked by weak C—H⋯O hydrogen bonds, generating C(8) and C(4) chains propagating along [100] and [010], respectively, which together generate (001) sheets.

Crystal structure of 2,2-di-chloro-1-(piperidin-1-yl)ethanone.

In the title compound, C7H11Cl2NO, the piperidine ring shows a chair conformation and the bond-angle sum at the N atom is 359.9°. The H atom of the di­chloro­methyl group is in an eclipsed conformation with respect to the carbonyl group (H—C—C=O = −5°). In the crystal, inversion dimers are linked by pairs of C—H⋯O hydrogen bonds between the di­chloro­methyl group and the carbonyl O atom, which generate R 2 2(8) loops. The dimers are linked into a ladder-like structure propagating in the [100] direction by short O⋯Cl [3.1084 (9) Å] contacts.