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author:("daniel, Maria")
1.  (R,R)-1-Acetyl-1′-(2,4,6-trinitro­phen­yl)-2,2′-bipyrrolidine 
The structure of the title mol­ecule, C16H19N5O7, is mainly determined by the steric effect of a bulky 2,4,6-trinitro­phenyl group attached to the N atom of a pyrrolidine ring. Both pyrrolidine rings adopt an envelope conformation, with one of the methylene C atoms as the flap in each case, and the N—C—C—N torsion angle along the bond connecting the two pyrrolidine rings is −174.9 (2)°. The benzene ring of the 2,3,5-trinitro­phenyl substituent is deformed and the r.m.s. deviation of its six atoms from the best plane is 0.026 Å. The N atoms of the two nitro groups in the ortho positions deviate from the best plane of the benzene ring by −0.033 (5) and 0.385 (5) Å. These groups, as well as the pyrrolidine ring, are twisted relative to the aromatic ring in the same direction, their best planes forming dihedral angles of 30.2 (2), 64.8 (1) and 46.6 (2)°, respectively, with the ring. An intra­molecular C—H⋯O hydrogen bond occurs. In the crystal, there is a short [O⋯C = 3.019 (4) Å] contact between a nitro O atom and a C atom of the benzene ring bearing the nitro group and a C—H⋯O inter­action between a methyl H atom and another nitro O atom.
PMCID: PMC3588260  PMID: 23476399
2.  N,N′-Bis(pyridin-2-yl)benzene-1,4-diamine–naphthalene (2/1) 
The asymmetric unit of the title compound, C10H8·2C16H14N4, consists of one mol­ecule of N,N′-bis­(pyridin-2-yl)benzene-1,4-diamine (PDAB) and one half of the centrosymmetric naphthalene mol­ecule. The PDAB mol­ecule adopts a non-planar conformation with an E configuration at the two partially double exo C N bonds of the 2-pyridyl­amine units. In the crystal, N—H⋯N hydrogen bonds between the PDAB mol­ecules generate a cyclic R 2 2(8) motif, leading to the formation of PDAB tapes extending along [100]. The tapes are arranged into (010) layers and the naphthalene mol­ecules are enclosed in cavities formed between the PDAB layers.
PMCID: PMC3238953  PMID: 22199802
3.  N,N′-Bis(pyridin-2-yl)benzene-1,4-diamine–quinoxaline (2/1) 
The asymmetric unit of the title compound, 2C16H14N4·C8H6N2, consits of one mol­ecule of N,N′-bis­(pyridin-2-yl)benzene-1,4-diamine (PDAB) and one half-mol­ecule of quinoxaline (QX) that is located around an inversion centre and disordered over two overlapping positions. The PDAB mol­ecule adopts a non-planar conformation with an E configuration at the two partially double exo C N bonds of the 2-pyridyl­amine units. In the crystal, these self-complementary units are N—H⋯N hydrogen bonded via a cyclic R 2 2(8) motif, creating tapes of PDAB mol­ecules extending along [010]. Inversion-related tapes are arranged into pairs through π–π stacking inter­actions between the benzene rings [centroid–centroid distance = 3.818 (1) Å] and the two symmetry-independent pyridine groups [centroid–centroid distance = 3.760 (1) Å]. The QX mol­ecules are enclosed in a cavity formed between six PDAB tapes.
PMCID: PMC3238910  PMID: 22199763
4.  A third polymorph of N,N′-bis­(pyridin-2-yl)benzene-1,4-diamine 
A third polymorph of the title compound, C16H14N4, has been obtained. The mol­ecule adopts a non-planar conformation with an E configuration at the two partially double exo C N bonds of the 2-pyridyl­amine units. Like in the triclinic form [Bensemann et al. (2002 ▶). New J. Chem. 26, 448–456], the recognition process between 2-pyridyl­amine units takes place through formation of a cyclic R 2 2(8) hydrogen-bond motif, leading to the creation of tapes parallel to [001].
PMCID: PMC3247481  PMID: 22220099
5.  Experimental and computational study on the reactivity of 2,3-bis[(3-pyridylmethyl)amino]-2(Z)-butene-1,4-dinitrile, a key intermediate for the synthesis of tribenzoporphyrazine bearing peripheral methyl(3-pyridylmethyl)amino substituents 
Monatshefte Fur Chemie  2011;142(6):599-608.
An earlier developed alkylating path leading to tetraalkylated diaminomaleonitrile derivatives was explored. Attempts to explain the reactivity of the representative dialkylated diaminomaleonitrile 2,3-bis[(3-pyridylmethyl)amino]-2(Z)-butene-1,4-dinitrile during the alkylation reaction were performed using X-ray and density functional theory (DFT) studies. The condensed Fukui functions accompanied by softness indices were found to be useful in explaining its reactivity observed during the reaction. The values of the Fukui functions and condensed softness for electrophilic attack calculated from Mulliken, Löwdin, and natural population analyses closely corresponded to the experimental observations. When 2,3-bis[(3-pyridylmethyl)amino]-2(Z)-butene-1,4-dinitrile disodium salt was treated with dimethyl sulfate at lower temperatures the alkylation reaction prevailed, whereas at higher temperatures the alkylating agent acted as a hydride anion acceptor, which favored the elimination reaction. The tetraalkylated dinitrile 2,3-bis[methyl(3-pyridylmethyl)amino]-2(Z)-butene-1,4-dinitrile was used in the synthesis of tribenzoporphyrazine bearing methyl(3-pyridylmethyl)amino groups, which was subsequently subjected to solvatochromic and metallation studies. The changes observed during metallation seem to result from the coordination of the 3-pyridyl group by a palladium ion. This could influence the configuration of the methyl(3-pyridylmethyl)amino moiety, causing more effective donation of a lone pair of electrons from peripheral nitrogen to the macrocyclic ring.
Graphical abstract
Electronic supplementary material
The online version of this article (doi:10.1007/s00706-011-0503-9) contains supplementary material, which is available to authorized users.
PMCID: PMC4495027  PMID: 26166858
Alkylations; Density functional theory; Diaminomaleonitrile; Tribenzoporphyrazine; X-ray structure determination
6.  p-Phenyl­enediamine and its dihydrate: two-dimensional isomorphism and mechanism of the dehydration process, and N—H⋯N and N—H⋯π inter­actions 
p-Phenyl­enediamine can be obtained as the dihydrate, C6H8N2·2H2O, (I), and in its anhydrous form, C6H8N2, (II). The asymmetric unit of (I) contains one half of the p-phenyl­ene­diamine mol­ecule lying about an inversion centre and two halves of water mol­ecules, one lying on a mirror plane and the other lying across a mirror plane. In (II), the asymmetric unit consists of one mol­ecule in a general position and two half mol­ecules located around inversion centres. In both structures, the p-phenyl­enediamine mol­ecules are arranged in layers stabilized by N—H⋯π inter­actions. The diamine layers in (I) are isostructural with half of the layers in (II). On dehydration, crystals of (I) transform to (II). Comparison of their crystal structures suggests the most plausible mechanism of the transformation process which requires, in addition to translational motion of the diamine mol­ecules, in-plane rotation of every fourth p-phenyl­enediamine mol­ecule by ca 60°. A search of the Cambridge Structural Database shows that the formation of hydrates by aromatic amines should be considered exceptional.
PMCID: PMC2855568  PMID: 20203409
7.  (Carbonato-κ2 O,O′)bis­(di-2-pyridyl­amine-κ2 N,N′)cobalt(III) bromide 
In the title compound, [Co(CO3)(C10H9N3)2]Br, a distorted octa­hedral coordination of the CoIII atom is completed by four N atoms of the two chelating di-2-pyridyl­amine ligands and two O atoms of the chelating carbonate anion. The di-2-pyridyl­amine ligands are nonplanar and the dihedral angles between the 2-pyridyl groups are 29.11 (9) and 37.15 (12)°. The coordination cation, which has approximate C 2 symmetry, is connected to the bromide ion via an N—H⋯Br− hydrogen bond. The ionic pair thus formed is further assembled into a dimer via N—H⋯O inter­actions about an inversion centre. A set of weaker C—H⋯O and C—H⋯Br− inter­actions connect the dimers into a three-dimensional network.
PMCID: PMC3100002  PMID: 21753946
8.  5-Methyl-3,6,7,8a-tetra­hydro-2H-diimidazo[1,2-c:1′,2′-e]pyrido[1,2-a][1,3,5]triazin-5-ium iodide 
The structure of the title compound, C12H16N5 +·I−, shows that the methyl­ation reaction with CH3I occurred at the imine N atom at position 5 of the 3,6,7,8a-tetra­hydro-2H-diimidazo[1,2-c:1′,2′-e]pyrido[1,2-a][1,3,5]triazine system. In the cation, the sp 3-hybridized C atom belonging to the fused dihydro­pyrine and dihydro-1,3,5-triazine rings deviates by 0.514 (3) Å from the best plane defined by the remaining cationic non-H atoms. The fused dihydro­pyridine and dihydro-1,3,5-triazine rings are each in a half-chair conformation with the sp 3-hybridized C atom as a flap. The iodide anion is 3.573 (2) Å from the methyl­ated N atom and exhibits five short C—H⋯I− contacts with distances less than 3.16 Å. The structure has been determined from a non-merohedral twin with twin law [−1 0 0 0 − 1 0 0.115 0 1], minor domain = 0.1559 (12).
PMCID: PMC2979596  PMID: 21579550
9.  Phenazine–naphthalene-1,5-diamine–water (1/1/2) 
The asymmetric unit of the title compound, C12H8N2·C10H10N2·2H2O, contains one half-mol­ecule of phenazine, one half-mol­ecule of naphthalene-1,5-diamine and one water mol­ecule. The phenazine and naphthalene-1,5-diamine mol­ecules are located on inversion centers. The water mol­ecules serve as bridges between the naphthalene-1,5-diamine mol­ecules and also between the naphthalene-1,5-diamine and phenazine mol­ecules. The naphthalene-1,5-diamine and water mol­ecules are connected via N—H⋯O and O—H⋯N hydrogen bonds, forming a T4(2) motif. They are arranged into a two-dimensional polymeric structure parallel to (10) in which the water mol­ecule is a single donor and a double acceptor, whereas the amino group is a double donor and a single acceptor in the hydrogen bonding. These two-dimensional assemblies alternate with the layers of phenazine mol­ecules arranged into a herringbone motif. Each phenazine mol­ecule is hydrogen bonded to two water mol­ecules and thus a three-dimensional framework of hydrogen-bonded mol­ecules is generated.
PMCID: PMC2972038  PMID: 21578891
10.  5-Amino-1-naphthol 
In the title compound, C10H9NO, the amino and the hydr­oxy groups act both as a single donor and a single acceptor in hydrogen bonding. In the crystal, mol­ecules are connected via chains of inter­molecular ⋯N—H⋯O—H⋯ inter­actions, forming a two-dimensional polymeric structure resembling the hydrogen-bonded mol­ecular assembly found in the crystal structure of naphthalene-1,5-diol. Within this layer, mol­ecules related by a translation along the a axis are arranged into slipped stacks via π–π stacking inter­actions [inter­planar distance = 3.450 (4) Å]. The amino N atom shows sp 3 hybridization and the two attached H atoms are located on the same side of the aromatic ring.
PMCID: PMC2971357  PMID: 21578535
11.  Bis(4,6-diamino­pyrimidin-2-yl) disulfide dimethyl sufoxide disolvate 
The title compound, C8H10N8S2·2C2H6SO, was obtained unintentionally during an attempt to prepare a thiol­ate derivative of trimethyl­tin. The complete disulfide mol­ecule is generated by twofold rotation symmetry and the C—S—S—C torsion angle around the S—S bond is −85.70 (10)°. The mol­ecules are connected via N—H⋯N hydrogen bonds into strongly corrugated layers parallel to (001), generating an R 2 2(8) motif. The solvent mol­ecule, which exhibits minor disorder of its S atom [site occupancies = 0.9591 (18) and 0.0409 (18)], is linked to this layer via a pair of N—H⋯O inter­actions.
PMCID: PMC2960530  PMID: 21201707
12.  Cholic acid–quinoxaline (2/1) 
In the title inclusion compound, 2C24H40O5·C8H6N2, the unit cell contains two mol­ecules of cholic acid (3α,7α,12α-trihydr­oxy-5β-cholan-24-oic acid) and one mol­ecule of quinoxaline which implies disorder of the quinoxaline in the space group P21. The amphiphilic mol­ecules of cholic acid assemble, in an anti­parallel arrangement, via O—H⋯O hydrogen bonds, into typical corrugated host bilayers which are lipophilic on the outside and lipophobic on the inside. The host framework belongs to the so called α-trans subtype. The quinoxaline mol­ecules are accommodated in lipophilic channels formed between neighboring bilayers with only van der Waals inter­actions between host and guest. There is a crystallographic twofold screw axis directed along an empty channel in the host framework; however, neighboring guests in any one channel are related by a unit-cell translation along the b axis. Thus, the overall structure is a 1:1 superposition of two such channels related by the crystallographic twofold screw axis.
PMCID: PMC2961426  PMID: 21202647
13.  Quinoxaline–3-amino­phenol–water (2/1/2) 
The asymmetric unit of the title compound, 2C8H6N2·C6H7NO·2H2O, contains two quinoxaline mol­ecules, one mol­ecule of 3-amino­phenol and two water mol­ecules which are hydrogen bonded to form a two-dimensional polymeric structure. Each of the symmetry-independent quinoxaline mol­ecules forms separate stacks of different symmetry. In one set of stacks, the mol­ecules are related by a screw axis and are slightly tilted [dihedral angle = 7.12 (1)°]. In the second set of stacks, adjacent mol­ecules are parallel and related by an inversion center [inter­planar distances = 3.376 (4) and 3.473 (4) Å].
PMCID: PMC2961097  PMID: 21202378

Results 1-13 (13)