Interplanar Angle Research Articles

Molecular Structure and Density Functional Theory Calculations of 3-(3-Nitrothien-2-yl)indole: Structural and Vibrational Analysis

An X-ray diffraction study along with crystal supramolecular analysis of 3-(3-nitrothien-2-yl)indole, I, were carried out. The crystals are orthorhombic; C12H8N2O2S; M = 244.26; a = 13.3286 (6) A, b = 7.5109 (4) A, c = 21.8144 (9) A; α = β = γ = 90°; V = 2183.83 (18) A3, d c = 1.486 g/cm3, Z = 8, space group Pbca. The crystal structure of the title compound consists of two planar rings, the indole ring and the substituted thiophene ring. The inter-planar angle between the indole ring system and thiophene ring is 34.39°. The dihedral angle of the NO2 plane and the thiophene plane is 5.09°. The crystal packing shows crystal supramolecularity in which molecules are connected via different C–H···O, N–H···C(π) intermolecular interactions with edge-to-face and offset-face-to-face aryl···aryl, interactions consolidating three-dimensional network. The molecular geometry and vibrational frequencies of (C12H8N2O2S) in the ground state have been calculated by using density functional method (DFT/B3LYP) with 6-311++G(d,p) basis set. The optimized geometric bond lengths and bond angles and IR stretching frequencies obtained show good agreement with the experimental data. The crystal structure reveals different crystal supramolecularity motifs via C–H···O, N–H···C(π) and edge-to-face and offset-face-to-face aryl···aryl, interactions consolidating three-dimensional network. Density functional method (DFT/B3LYP) with 6-311++G(d,p) basis set of the obtained optimized geometric and IR stretching frequencies show good agreement with the experimental data.

What can we learn from artificial special pairs?

Plants and photosynthetic bacteria obtain their energy from sunlight or surrounding radiation. Their photosynthetic membranes are composed of a much elaborated series of antenna molecules based on chlorophylls or bacteriochlorophylls, carotenoids playing multiple roles, various electron transport accessories, and central special pairs. The latter components are the most difficult to mimic with exactitude because the structure−property relationship depends on many factors including interplanar distance, slip angle, substituents, metal, and axial ligand. To this list of factors to control with quasi-perfection, one should also add the thermal activation (i.e., temperature). Over the past 15 years or so (2001–2013), an intensive collaboration with Professor Roger Guilard (Université de Bourgogne, Dijon) dealt with elucidating the role of each parameter to provide the best design of artificial special pairs capable of responding or behaving like the natural special pairs, namely with regards with the antenna effect. The latest feature is one of the defence mechanisms slowing down the rate for the primary electron transfer from the special pair to the electron transport accessories. This review highlights the advances in this challenging area of mimicry of the photophysical events in biological systems, namely the artificial special pairs designed in our laboratory for the antenna processes.

From N,N-diphenyl-N-naphtho[2,1-b]thieno[2,3-b:3′,2′-d]dithiophene-5-yl-amine to propeller-shaped N,N,N-tri(naphtho[2,1-b]thieno[2,3-b:3′,2′-d]dithiophene-5-yl)-amine: syntheses and structures

Three unique propeller-shaped helicenyl amines compounds: N,N-diphenyl-N-naphtho[2,1-b]thieno[2,3-b:3′,2′-d]dithiophene-5-yl-amine (1), N-phenyl-N,N-di(naphtho[2,1-b]thieno[2,3-b:3′,2′-d]dithiophene-5-yl)amine (2), and N,N,N-tri(naphtho[2,1-b]thieno[2,3-b:3′,2′-d]dithiophene-5-yl)amine (3) were efficiently synthesized by Wittig reaction and oxidative photocyclization. The crystal structures of 1, 2 and molecular configuration optimization (DFT-B3LYP/6-31+G(d)) of 3 reveal that the steric hindrance from the moiety of trithia[5]helicene effectively forces the nitrogen atom and the three bonded carbon atoms to coplanar and the interplanar angles of the facing terminal thiophene ring and benzene ring becoming larger when the helical arm increased from 1 to 3. Electrochemical properties and UV–vis absorption behaviors of 1, 2, 3 were primarily determined by the moiety of trithia[5]helicene.

5,6-Dimethyl-2-(5-methyl-thio-phen-2-yl)-1-[(5-methyl-thio-phen-2-yl)meth-yl]-1H-benzimidazole.

The title mol­ecule, C20H20N2S2, is T-shaped and consists of a nearly flat 5,6-dimethyl-2-(5-methyl­thio­phen-2-yl)benzimidazole system approximately perpendicular to the 5-methyl­thio­phen-2-ylmethyl substituent. The 5,6-dimethyl-2-(5-meth­yl­thio­phen-2-yl)benzimidazole system is rotationally disordered about the two imidazole N atoms as approximated by a twofold rotation axis with a refined major/minor occupancy ratio of 0.884 (2):0.116 (2). The benzimidazole ring system is essentially planar, the largest deviations being 0.026 (2) and 0.044 (18) Å in the major and minor components, respectively. The inter­planar angles between the benzimidazole unit and the 5-methyl­thio­phen-2-yl substituent are 10.8 (3) and 8(3)° in the major and minor components, respectively, and the corresponding angles with the 5-methyl­thio­phen-2-ylmethyl substituent are 88.12 (8) and 89.5 (4)°. In the crystal, mol­ecules are oriented with their 2-(5-methyl­thio­phen-2-yl)benzimidazole mean planes approximately parallel to (11) and appear to be held together by π–π [2-thiophene⋯imidazole centroid–centroid distance = 4.1383 (7) Å] and C—H⋯π contacts. A weak C—H⋯N hydrogen bond generates infinite chains parallel to [100].

Progressive acylation of pyrene engineers solid state packing and colour via C-H···H-C, C-H···O and π-π interactions.

Quantum theory of atoms-in-molecules and Hirshfeld surface analyses indicated an increase in the extent of (i) C-H···H-C; (ii) C-H···O, (iii) π-π interactions and a decrease in the extent of (i) σ-π interaction, (ii) an interplanar angle between the vicinal pyrene units in a series of acetylpyrene derivatives offering blue-green-orange emissive crystals.

4-Acetyl-3-[2-(ethoxycarbonyl)phenyl]sydnone

Sydnones, which contain a mesoionic five-membered heterocyclic ring, are more stable if synthesized with an aromatic substutuent at the N3 position. In the title compound {sys­tematic name: 4-acetyl-3-[2-(eth­oxy­carbon­yl)phen­yl]-1,2,3-oxa­diazol-3-ylium-5-olate}, C13H12N2O5, the aromatic substitutent is 2-(eth­oxy­carbon­yl)phenyl. Intra- and inter­molecular hydrogen bonds are observed. The inter­planar angle between the sydnone and benzene rings is 71.94 (8)°. π-ring⋯carbon­yl inter­actions of 3.2038 (16) Å arise between the sydnone ring and a symmetry-related C=O group.

2-Amino-5-methyl-3-(2-oxo-2-phenylethyl)-7-phenyl-4,5,6,7-tetrahydro-3H-[1,2,4]triazolo[1,5-a]pyrimidin-8-ium bromide ethanol monosolvate

In the title compound, C20H22N5O+·Br−·C2H6O, the tetra­hydro­pyrimidine ring of the bicyclic cation adopts a half-chair conformation with an equatorial orientation of the phenyl and methyl substituents. The amino group is nearly coplanar with the 1,2,4-triazole ring [interplanar angle = 4.08 (8)°] and has a slightly pyramidal configuration. The mean planes of the triazole ring and the benzene ring of the phenacyl group form a dihedral angle of 88.58 (7)°. In the crystal, N—H⋯Br, N—H⋯O and O—H⋯Br hydrogen bonds link the cations, anions and ethanol mol­ecules into layers parallel to the bc plane.

Comparison of the monomer structure of the FMN-binding protein from Desulfovibrio vulgaris obtained by NMR and molecular dynamics simulation approaches

Flavin mononucleotide (FMN)-binding proteins (FBPs) play an important role in the electron transport process in bacteria. In this study, the structures of the FBP from Desulfovibrio vulgaris (DvFBP) (Miyazaki F) were compared between those obtained experimentally by nuclear magnetic resonance (NMR) spectroscopy and those derived from molecular dynamics simulations (MDSs). A high-residue root of mean square deviation (RMSD) was observed in residues located at both sides of the wings (Gly22, Glu23, Asp24, Ala59, Arg60, Asp61, Glu62, Gly75, Arg76, Asn77, Gly78 and Pro79), while a low-residue RMSD was found in residues located in a hollow of the structure (Asn12, Glu13, Gly14, Val15, Val16, Asn30, Thr31, Trp32, Asn33, Ser34, Gly69, Ser70, Arg71 and Lys72). Inter-planar angles between the Phe7 and Iso and between the Phe7 and Trp106 residues were remarkably different between the MDS- and NMR-derived DvFBP structures. Distribution of the torsion angles around the covalent bonds in the aliphatic chain of FMN was similar in the MDS- and NMR-derived structures, except for those around the C1′–C2′ and C5′–O5′ bonds. Hydrogen bond formation between IsoO2 and the Gly49 or Gly50 peptide NH was formed in both the NMR- and MDS-derived structures. Overall, the MDS-derived structures were found to be considerably different from the NMR-derived structures, which must be considered when the photoinduced electron transfer in flavoproteins is analysed with MDS-derived structures.

2,2′-[(4-Methyl-2-phenylimidazolidine-1,3-diyl)bis(methylene)]diphenol

The methyl-substituted imidazolidine ring of the title compound, C24H26N2O2, adopts an envelope conformation with the N atom adjacent to the methyl­ene group as the flap. The meth­yl–ethyl­ene fragment in this ring is disordered over two positions with an occupancy ratio of 0.899 (4):0.101 (4). The hy­droxy­benzyl groups are inclined at 71.57 (15) and 69.97 (19)° to the mean plane of major disorder component of the heterocyclic ring with an inter­planar angle between the two hy­droxy­benzyl groups of 66.00 (5)°. The phenyl substit­uent approaches a nearly perpendicular orientation relative to the mean plane of the imidazolidine ring, making a dihedral angle of 75.60 (12)°. This conformation is stabilized by two intra­molecular O—H⋯N bonds, which generate S(6) ring motifs.

Synthesis and structural properties of hexaaza[5]helicene containing two [1,2,3]triazolo[1,5-a]pyridine moieties

We have synthesized a novel hexaaza[5]helicene in a straightforward way from neocuproine. The crystal structure has been elucidated with direct-space strategy TALP which demonstrates the power of the powder X-ray diffraction technique. In this crystal structure it is possible to see an interplanar angle of 33(1)° between the two triazolopyridine rings. The centrosymmetric crystal structure is a racemic mixture, but the resolution was not possible due to a ring-chain isomerization in a solution that produces a dynamic racemization.

2-Methyl-1,1-diphenyl-2-[(4S)-4-phenyl-4,5-dihydro-1,3-oxazol-2-yl]propan-1-ol

In the title compound, C25H25NO2, the phenyl ring on the 1,3-oxazole ring is disordered over two positions with occupancies of 0.600 (4) and 0.400 (4). The inter­planar angle between these two disordered rings is 77.8 (2)°. There is an intra­molecular O—H⋯N hydrogen bond of moderate strength. In the crystal, C—H⋯π inter­actions interconnect neighbouring molecules. The absolute structure has been derived from the known absolute structure of the reagents.

N-(2-Methoxyphenyl)phthalamic acid

The title compound, C14H13NO3, adopts a twisted conformation in the crystal, with an inter­planar angle between the two benzene rings of 87.30 (5)°. Mol­ecules within the structure are linked via O—H⋯O inter­actions, forming a hydrogen-bonded chain motif with graph set C(7) along the glide plane in the [001] direction.

Structural, Thermodynamic, and Kinetic Aspects of the Polymorphism of Trimethylthiourea: The Influence of Kinetics on the Transformations between Polymorphs

Trimethylthiourea crystallizes in two different polymorphic modifications. Polymorph I crystallizes in the monoclinic space group P21/c with Z = 8, whereas polymorph II crystallizes in the alternative setting of the same space group, P21/n with Z = 4. Both polymorphs form chains of molecules linked by hydrogen bonds N–H···S═C via glide planes, with translational repeats after four molecules (the two independent molecules alternate) or two molecules, respectively. Interplanar angles between molecules in the chain differ appreciably between I and II, and for I, one hydrogen bond is very nonplanar with respect to the N2C═S acceptor plane. Solvent-mediated conversion experiments prove that polymorph II is the thermodynamically stable polymorph at room temperature, where I is metastable, and that I can be obtained by solidification of the melt. On heating, I transforms slowly into II with no detectable transfer of energy, and on further heating, melting of this polymorph is observed. DSC experiments reveal tha...

3-Methyl-1-tosyl-1H-indole-2-carbaldehyde

The title indole derivative, C17H15NO3S, crystallizes with two independent mol­ecules in the asymmetric unit. The benzene ring of the tosyl group is almost perpedicular to the indole ring in both mol­ecules, with inter­planar angles of 82.60 (5)° and 81.82 (6)°. The two mol­ecules are, as a consequence, able to form an almost centrosymmetric non-bonded dimer, in which the molecules are linked by pairs of C—H⋯π inter­actions. The crystal structure displays a three-dimensional network of C—H⋯O inter­actions. A π–π inter­action occurs between inversion-related indole rings with a centroid–centroid distance of 3.6774 (16) Å and an inter­planar angle of 1.53 (15)°. This inter­action leads to a stacking of mol­ecules along the a axis.

Crystal structures of three 4-[3-(XC6H4)-hexahydro[1,3] oxazolo[3,4-a]pyridin-1-yl]-2,8-bis(trifluoromethyl)quinolines (X = 3-MeO, 4-MeO and 4-HO)

The crystal structures of three racemic 4-{3- (X-phenyl)hexahydro[1,3]oxazolo[3,4-a]pyridin-1-yl}-2,8- bis (trifluoromethyl)quinolines, 2, namely (2: X = 3-MeO, 4-MeO and 4-HO), prepared from mefloquine and XC 6 H 5 CHO, are reported. All three molecules were previously reported to be active in in-vitro studies against the multidrug-resistant tuberculosis strain T113. In each of the three molecules, the piperidinyl ring has a chair shape with substituents in equatorial sites and the 1,3-oxazolidinyl ring exhibit deviations from planarity. All molecules have “F’’ shape conformations with the X-phenyl and quinoline rings lying on one side of the best plane through the fused oxazolidine-piperidine rings, and in an arrangement approaching open butterfly wings. However there are differences in the inter-planar angles. No correlation was established between the anti-TB activity and the molecular conformation. Compound (2: X = 4-MeO) has a onedimensional structure generated from C-F ... π(pyridine) and C-H ... π(methoxyphenyl) interactions. Both (2: X = 3-MeO) and (2: X = 4-HO) have three dimensional structures. The supramolecular arrangements in (2: X = 3-MeO) are derived from C-H ... O(oxazolidine), C-H ... F and C-H ... π(phenyl of quinoline) interactions and those for (2: X = 4-HO) from O-H ... N(piperidine), C-H ... O(hydroxyl), C-H ... F, C-H ... π(phenyl of quinoline), C-F ... π(pyridine), C-F ... π(imine) and p(methoxyphenyl) ... π(methoxyphenyl) interactions.

Conformational influence of quinoline moieties in the crystal packing of bis(quinolinecarboxamide)alkane derivatives

Six new compounds of the homologous series of N,N′-bis(2-quinolinecarboxamide)alkane (4a–c) and N,N′-bis(6-quinolinecarboxamide)alkane (5a–c) derivatives having two, four and six carbon atoms in the alkyl spacer were synthesized and their crystal structures were determined by single crystal X-ray diffraction. These solid-state structures have been analyzed finding that the two series exhibit interesting differences between them. The remarkable preference of the bis(6-quinolinecarboxamide)alkanes to form one- or two-dimensional networks via N–H⋯O intermolecular hydrogen bonds appears total or partially disrupted by the intramolecular N–H⋯Nquinoline hydrogen bond in bis(2-quinolinecarboxamide)alkanes. These interactions, theoretically sorted as a ‘very weak and purely electrostatic’, seems to play a fundamental role in the crystal packing of bis(2-quinolinecarboxamide) derivatives. On the other hand, the rationalization of the bis(6-quinolinecarboxamide) structures are completely in agreement with the statement that the amide-to-amide hydrogen bond formation and network (β-sheets or 4,4-network), in these systems, depends on the interplanar angle between the amide group and the heterocyclic ring.

True symmetry or pseudosymmetry: 5-amino-1-(4-methylphenylsulfonyl)-4-pyrazolin-3-one and a comparison with its 1-phenylsulfonyl analogue

The title compound, C(10)H(11)N(3)O(3)S, (I), crystallizes as the NH tautomer. The two rings subtend an interplanar angle of 72.54 (4)°. An intramolecular hydrogen bond is formed from the NH(2) group to a sulfonyl O atom. The molecular packing involves layers of molecules parallel to the bc plane at x ≃ 0, 1 etc., with two classical linear hydrogen bonds (amino-sulfonyl and pyrazoline-carbonyl N-H...O) and a further interaction (amino-sulfonyl N-H...O) completing a three-centre system with the intramolecular contact. The analogous phenyl derivative, (II) [Elgemeie, Hanfy, Hopf & Jones (1998). Acta Cryst. C54, 136-138], crystallizes with essentially the same unit cell and packing pattern, but with two independent molecules that differ significantly in the orientation of the phenyl groups. The space group is P2(1)/c for (I) but P2(1) for (II), which is thus a pseudosymmetric counterpart of (I).

17-Hydroxy-1,8-dimethyl-17-azapentacyclo[6.6.5.02,7.09,14.015,19]nonadeca-2,4,6,9(14),10,12-hexaene-16,18-dione

In the title compound, C20H17NO3 (alternative name: N-hy­droxy-9,10-dimethyl-9,10-ethano­anthracene-11,12-dicarboximide), the rigid ethano­anthracene-dicarboximide moiety has a roof-shaped geometry, the inter­planar angle between the two terminal phenyl rings being 124.9 (6)°. In the crystal, mol­ecules are linked via O—H⋯O hydrogen bonds, forming chains along [010]. C—H⋯O and C—H⋯π inter­actions link adjacent chains, leading to the formation of a three-dimensional structure.

5-[(Z)-2,3-Dimethoxybenzylidene]-1,2,4-triazolo[3,2-b][1,3]thiazol-6(5H)-one

The title compound, C13H11N3O3S, was synthesized from 1H-1,2,4-triazole-5-thiol in a one pot reaction. The fused thia­zolo[3,2-b][1,2,4]triazole system is essentially coplanar with the benzene ring: they enclose an inter­planar angle of 1.37 (13)°. The olefinic double bond is in a Z conformation. In the crystal, C—H⋯N hydrogen bonds link the mol­ecules into double layers parallel to the ab plane.

6-Bromo-4-[2-(4-fluorobenzylidene)hydrazin-1-ylidene]-1-methyl-3,4-dihydro-1H-2λ6,1-benzothiazine-2,2-dione

In the title compound, C16H13BrFN3O2S, the dihedral angle between the aromatic rings is 2.55 (19)° and the C=N—N=C torsion angle is 178.9 (3)°. The conformation of the thia­zine ring is an envelope, with the S atom displaced by −0.811 (3) Å from the mean plane of the other five atoms (r.m.s. deviation = 0.042 Å). In the crystal, C—H⋯O inter­actions link the mol­ecules and weak aromatic π–π stacking between the fluoro­benzene and bromo­benzene rings [centroid–centroid separation = 3.720 (2) Å and inter­planar angle = 2.6 (2)°] is also observed.