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1.  New aryloxybenzylidene ruthenium chelates – synthesis, reactivity and catalytic performance in ROMP 
New phenoxybenzylidene ruthenium chelates were synthesised from the second generation Grubbs catalysts bearing a triphenylphosphine ligand (or its para-substituted analogues) by metathesis exchange with substituted 2-vinylphenols. The complexes behave like a latent catalyst and are characterized by an improved catalytic behaviour as compared to that of the known analogues, i.e., they exhibit high catalytic inactivity in their dormant forms and a profound increase in activity after activation with HCl. The strong electronic influence of substituents in the chelating ligand on the catalytic activity was demonstrated. The catalytic properties were tested in ROMP of cyclooctadien (COD) and a single selected norbornene derivative.
PMCID: PMC4660962  PMID: 26664610
chemoactivation; latent catalysts; metathesis; ROMP; ruthenium
2.  Anharmonicity and isomorphic phase transition: a multi-temperature X-ray single-crystal and powder diffraction study of 1-(2′-aminophenyl)-2-methyl-4-nitroimidazole 
Iucrj  2014;1(Pt 2):110-118.
Multi-temperature single-crystal and powder diffraction experiments on 1-(2′-aminophenyl)-2-methyl-4-nitroimidazole show that this crystal undergoes an isomorphic phase transition with the coexistence of two phase domains over a wide temperature range. The anharmonic approach was the only way to model the resulting disorder.
The harmonic model of atomic nuclear motions is usually enough for multipole modelling of high-resolution X-ray diffraction data; however, in some molecular crystals, such as 1-(2′-aminophenyl)-2-methyl-4-nitro-1H-imidazole [Paul, Kubicki, Jelsch et al. (2011 ▶). Acta Cryst. B67, 365–378], it may not be sufficient for a correct description of the charge-density distribution. Multipole refinement using harmonic atom vibrations does not lead to the best electron density model in this case and the so-called ‘shashlik-like’ pattern of positive and negative residual electron density peaks is observed in the vicinity of some atoms. This slight disorder, which cannot be modelled by split atoms, was solved using third-order anharmonic nuclear motion (ANM) parameters. Multipole refinement of the experimental high-resolution X-ray diffraction data of 1-(2′-aminophenyl)-2-methyl-4-nitro-1H-imidazole at three different temperatures (10, 35 and 70 K) and a series of powder diffraction experiments (20 ≤ T ≤ 300 K) were performed to relate this anharmonicity observed for several light atoms (N atoms of amino and nitro groups, and O atoms of nitro groups) to an isomorphic phase transition reflected by a change in the b cell parameter around 65 K. The observed disorder may result from the coexistence of domains of two phases over a large temperature range, as shown by low-temperature powder diffraction.
PMCID: PMC4062092  PMID: 25075327
anharmonicity; isomorphic phase transition; experimental charge density; X-ray closed-circuit helium cryostat; Hansen–Coppens model; multiple-temperature powder diffraction
3.  2-(4-Methyl­phen­yl)-2-oxoethyl 3-bromo­benzoate 
The mol­ecule of the title compound, C16H13BrO3, is built of two approximately planar fragments, viz. 3-bromo­benzoate [maximum deviation = 0.055 (2) Å and 2-oxo-2-p-tolyl­ethyl [maximum deviation = 0.042 (2) Å], inclined by 46.51 (7)°. In the crystal, weak C—H⋯O hydrogen bonds and Br⋯Br contacts [3.6491 (7) Å] connect the mol­ecules into infinite layers parallel to (-221).
PMCID: PMC3589039  PMID: 23476275
4.  {4,4′,6,6′-Tetrachloro-2,2′-[2,2-dimethyl­propane-1,3-diylbis(nitrilo­methanylyl­idene)]diphenolato}dioxidomolyb­denum(VI) 
The asymmetric unit of the title compound, [Mo(C19H16Cl4N2O2)O2], comprises two independent mol­ecules (A and B). The geometry around the MoVI atom is distorted octa­hedral in each complex mol­ecule, supported by two oxide O atoms and the N2O2 donor atoms of the coordinating ligand. The dihedral angle between the benzene rings is 74.96 (11) Å for mol­ecule A and 76.05 (11) Å for mol­ecule B. In the crystal, the B mol­ecules are linked by pairs of C—H⋯Cl hydrogen bonds, forming inversion dimers. The crystal structure is further stabilized by C—H⋯π inter­actions. An inter­esting feature of the crystal structure is a Cl⋯Cl contact [3.3748 (18) Å], which is shorter than the sum of the van der Waals radii of Cl atoms (3.50 Å).
PMCID: PMC3470140  PMID: 23125584
5.  1-[Bis(4-fluoro­phen­yl)meth­yl]piperazine 
In the title mol­ecule, C17H18F2N2, the dihedral angle between the benzene rings is 73.40 (3)°. The piperazine ring is close to an ideal chair conformation and the N—H hydrogen is in an equatorial position. In the crystal, molecules are linked via weak C—H⋯F hydrogen bonds.
PMCID: PMC3435841  PMID: 22969687
6.  4-Phenyl-1H-imidazole-2(3H)-thione 
In the asymmetric unit of the title compound, C9H8N2S, there are four symmetry-independent mol­ecules (Z′ = 4). The geometrical features of these mol­ecules are quite similar: in the normal probability plots the R 2 correlation factors for bond lengths and angles are generally around 0.95. The twist angles between the imidazole and phenyl rings (which are planar within 3σ) range from 9.0 (6) to 13.1 (5)°. In the crystal, pairs of independent molecules are joined by linear N—H⋯S and weak C—H⋯S hydrogen bonds, forming infinite ribbons, of the type ∼ABABAB∼ and ∼CDCDCD∼, propagating along [110]. Second-order hydrogen-bonded R 2 2(8) rings are formed via inter­weaving infinite C 2 2(8) chains.
PMCID: PMC3379282  PMID: 22719480
7.  4-[(4-Benzyl­oxybenzyl­idene)amino]-1,5-dimethyl-2-phenyl-1H-pyrazol-3(2H)-one 
In the title mol­ecule, C25H23N3O2, two terminal phenyl rings are twisted by 50.20 (6) and 71.26 (5)° from the mean plane (r.m.s. deviation = 0.032 Å) of the central benzyl­idene–amino–pyrazolone fragment. The N atoms of the pyrazole ring have a pyramidal environment, the sums of the valence angles around them being 353.5 (2) and 347.3 (2)°. The crystal structure is stabilized by C—H⋯O interactions.
PMCID: PMC3344463  PMID: 22590225
8.  (R)-Doxylaminium (R,R)-tartrate 
In the title compound (systematic name: (R)-dimeth­yl{2-[1-phenyl-1-(pyridin-2-yl)eth­oxy]eth­yl}aza­nium (R,R)-3-carb­oxy-2,3-dihy­droxy­propano­ate), C17H23N2O+·C4H5O6 −, the doxylaminium cation is protonated at the N atom. The tartrate monoanions are linked by short, almost linear O—H⋯O hydrogen bonds into chains extended along [100]. These chains are inter­linked by anion–pyridine O—H⋯N hydrogen bonds into a two-dimensional grid structure. WeakC—H⋯O inter­actions also play a role in the crystal packing. An intra­molecular hy­droxy–carboxyl­ate O—H⋯O hydrogen bond influences the conformation of the anion: the hydrogen-bonded fragment is almost planar, the maximum deviation from the mean plane being 0.059 (14) Å. In the cation, the aromatic rings are almost perpendicular [dihedral angle = 84.94 (8)°] and the conformation of the O—C—C—N chain is gauche(−), the dihedral angle is −76.6 (2)°. The absolute configuration was assigned on the basis of known chirality of the parent compound.
PMCID: PMC3344015  PMID: 22589924
9.  Ethyl N-(2-benzoyl-4-chloro­phen­yl)­ethane­carboximidate 
In the title compound, C17H16ClNO2, the N=C—O—C—C fragment is planar within 0.029 (1) Å, and makes dihedral angles of 66.71 (8) and 59.61 (8)° with the planes of the chloro­phenyl and benzoyl rings, respectively. The carbonyl C=O bond is not coplanar with either of the aromatic rings; it makes angles of 42.5 and 23.5° with the normals to the ring planes. In the crystal, very weak C—H⋯O, C—H⋯Cl, C—H⋯π and π–π [inter­planar distance = 3.53 (1) Å] inter­actions are observed.
PMCID: PMC3297957  PMID: 22412760
10.  Tramadolium picrate 
In the title salt {systematic name: [2-hy­droxy-3-(3-meth­oxy­phen­yl)cyclo­hexyl­meth­yl]dimethyl­aza­nium 2,4,6-trinitro­phenol­ate}, C16H26NO2 +·C6H2N3O7 −, the cation is protonated at the N atom. The cyclo­hexane ring adopts a chair conformation with the hy­droxy substituent in an axial position. In the crystal, O—H⋯O and N—H⋯O hydrogen bonds link the cations and anions into supra­molecular chains along [100].
PMCID: PMC3297323  PMID: 22412513
11.  Bis[μ-4-(2-oxidobenzyl­idene)thio­semi­carbazidato-κ4 S,N 1,O:O]bis­[(pyridine-κN)zinc] 
In the title compound, [Zn2(C8H7N3OS)2(C5H5N)2], the Zn2O2 ring has a flattened roof shape, with the roof angle equal to 10.10 (6)°. The thio­semicarbazones act as tridentate ligands to one ZnII atom, with the O atoms additionally in bridging positions to the second ZnII atom. Both ZnII atoms are five-coordinated; the coordination polyhedra are close to square pyramids, with the pyridine N atoms at apical positions. Two inter­molecular N—H⋯N and one relatively weak N—H⋯S hydrogen bond, together with C—H⋯S weak inter­actions, connect the mol­ecules into a three-dimensional network.
PMCID: PMC3274852  PMID: 22346799
12.  [S-Allyl-4-(4-hy­droxy-2-oxidobenzyl­idene-κO)-1-(2-oxidobenzyl­idene-κO)isothio­semicarbazidato-κ2 N 1,N 4](ethanol-κO)dioxido­uranium(VI) ethanol monosolvate 
In the title compound, [U(C18H15N3O3S)O2(C2H5OH)]·C2H5OH, the UVI ion is in a distorted penta­gonal–bipyramidal coordination geometry, with two oxide O atoms in axial sites. Two N and two O atoms of the tetra­dentate ligand and an O atom of an ethanol ligand form the equatorial plane. The dihedral angle between the mean planes of the two benzene rings is 34.8 (3)°. In the crystal, relatively strong O—H⋯O hydrogen bonds connect the complex and ethanol solvent mol­ecules into alternating centrosymmetric R 2 2(8) and R 4 4(16) ring motifs, forming chains along [100]. Weak inter­molecular C—H⋯O hydrogen bonds are also present.
PMCID: PMC3238725  PMID: 22199602
13.  Bromidotris(triphenyl­phosphane)silver acetonitrile monosolvate monohydrate 
In the title compound, [AgBr(C18H15P)3]·C2H3N·H2O, the coordination of the Ag atom is close to ideal tetra­hedral, with the three Ag—P bond lengths almost equal [2.5441 (10), 2.5523 (9) and 2.5647 (10) ° A] and the Ag—Br bond slightly longer [2.7242 (5) Å]. The coordination tetra­hedron is slightly flattened, the Ag atom is closer to the PPP plane; the P—Ag—P angles are wider than the Br—Ag—P angles. The voids in the crystal structure are filled with ordered acetonitrile solvent mol­ecules. The remaining electron density was inter­preted as a water mol­ecule, disordered over three alternative positions. Neither of the solvent mol­ecules is connected by any directional specific inter­actions with the complex.
PMCID: PMC3246938  PMID: 22219758
14.  1-(3-Chloro­phen­yl)-2-methyl-4-nitro-1H-imidazole-5-carboxamide 
In the crystal structure of the title compound, C11H9ClN4O3, pairs of N—H⋯N(imidazole) hydrogen bonds connect the mol­ecules into centrosymmetric dimers, which are further connected by N—H⋯O(carbamo­yl) hydrogen bonds into C(4) chains along [010]. Inter­play of these two kinds of hydrogen bonds connect the mol­ecules into layers perpendicular to [101]. The imidazole [maximum deviation 0.0069 (9) Å] and phenyl rings are inclined at a dihedral angle of 58.44 (6)°; the nitro group is almost coplanar [dihedral angle 5.8 (2)°] with the imidazole ring while the carbamoyl group is almost perpendicular [70.15 (13)°] to it.
PMCID: PMC3201265  PMID: 22058768
15.  5-Chloro-1-phenyl-1H-pyrazol-4-amine 
In the crystal structure of the title compound, C9H8ClN3, amino–pyrazole N—H⋯N hydrogen bonds connect the mol­ecules along the [010] direction; the chains interact with each other only by van der Waals-type inter­actions. The pyrazole and phenyl rings are inclined at a dihedral angle of 45.65 (6)°
PMCID: PMC3200699  PMID: 22065135
16.  (2E)-3-(3-Bromo-4-meth­oxy­phen­yl)-1-(4-fluoro­phen­yl)prop-2-en-1-one 
In the title compound, C16H12BrFO2, the dihedral angle between the aromatic rings is 23.75 (12)° and the dihedral angle between the prop-2-en-1-one fragment and the fluorobenzene ring is 20.9 (2)°. In the crystal, only van der Waals interactions occur.
PMCID: PMC3089233  PMID: 21754410
17.  High regularity of Z-DNA revealed by ultra high-resolution crystal structure at 0.55 ņ 
Nucleic Acids Research  2011;39(14):6238-6248.
The crystal structure of a Z-DNA hexamer duplex d(CGCGCG)2 determined at ultra high resolution of 0.55 Å and refined without restraints, displays a high degree of regularity and rigidity in its stereochemistry, in contrast to the more flexible B-DNA duplexes. The estimations of standard uncertainties of all individually refined parameters, obtained by full-matrix least-squares optimization, are comparable with values that are typical for small-molecule crystallography. The Z-DNA model generated with ultra high-resolution diffraction data can be used to revise the stereochemical restraints applied in lower resolution refinements. Detailed comparisons of the stereochemical library values with the present accurate Z-DNA parameters, shows in general a good agreement, but also reveals significant discrepancies in the description of guanine-sugar valence angles and in the geometry of the phosphate groups.
PMCID: PMC3152349  PMID: 21459852
18.  (2E)-3-(3-Bromo-4-meth­oxy­phen­yl)-1-(4-methyl­phen­yl)prop-2-en-1-one 
The overall shape of the mol­ecule of the title compound, C17H15BrO2, can be described by the dihedral angles between three planar fragments: 1-bromo-2-meth­oxy­phenyl ring [maximum deviation = 0.003 (2) Å], the central prop-2-en-1-one chain [maximum deviation = 0.005 (2) Å], and the methyl­phenyl ring [maximum deviation = 0.004 (2) Å]. The terminal planes are twisted by 10.37 (12)°, while the central plane is almost coplanar with the methyl­phenyl ring [3.30 (13)°], but the dihedral angle with the other phenyl ring is significantly larger [8.76 (16)°]. In the crystal, mol­ecules are linked into chains along [001] by three C—H⋯O hydrogen bonds. These chains inter­act with each other by means of weak π–π contacts [centroid–centroid distances = 3.73 (1) and 3.44 (1) Å]. An inter­molecular C—H⋯Br inter­action also occurs.
PMCID: PMC3099759  PMID: 21754040
19.  N-[2-(Acetamido)­eth­yl]-2-hy­droxy­benzamide 
In the title mol­ecule, C11H14N2O3, an intra­molecular O—H⋯O hydrogen bond closes an almost planar [maximum deviation = 0.022 (13) Å] six-membered ring and enforces the cis conformation of the keto group with respect to the hy­droxy substituent. In the crystal, inter­molecular N—H⋯O hydrogen bonds link the moleclues into ribbons extended along [10]. Weak inter­molecular C—H⋯O inter­actions further consolidate the crystal packing.
PMCID: PMC3051945  PMID: 21522324
20.  (1RS,6SR)-Ethyl 4-(2,4-dichloro­phen­yl)-6-(4-fluoro­phen­yl)-2-oxocyclo­hex-3-ene-1-carboxyl­ate 
There are two symmetry-independent mol­ecules in the asymmetric unit of the title compound, C21H17Cl2FO3. Both these mol­ecules are very similar: the normal probability plots for bond lengths, angles and even for torsion angles show that the differences are of a statistical nature. A pseudocentre of symmetry is located between the symmetry-independent mol­ecules at [0.245 (1), 0.535 (19), 0.909 (1)]. The cyclo­hexene rings have slightly distorted sofa conformations in both mol­ecules and the two benzene rings are inclined by dihedral angles of 61.33 (14) and 62.85 (14)°. In the crystal, relatively short inter­molecular C—H⋯O inter­actions join mol­ecules into homomolecular (i.e. ⋯AAA⋯ and ⋯BBB⋯) chains along the b axis. These chains are inter­connected by further heteromolecular C—H⋯O inter­actions.
PMCID: PMC3051448  PMID: 21523109
21.  1-Methyl­piperazine-1,4-diium dipicrate 
In the crystal structure of the title compound [systematic name: 1-methyl­piperazine-1,4-diium bis­(2,4,6-trinitro­phen­ol­ate)], C5H14N2 2+·2C6H2N3O7 −, the ionic components are connected by relatively strong N—H⋯O hydrogen bonds into centrosymmetric six-membered conglomerates, which comprise two dications and four anions. Besides Coulombic inter­actions, only weak C—H⋯O inter­actions and some stacking between picrates (separation between the planes of ca. 3.4 Å but only a small overlapping) can be identified between these ‘building blocks’ of the crystal structure. The piperazine ring adopts a chair conformation with the methyl substituent in the equatorial position. In the picrate anions, the twist angles of the nitro groups depend on their positions relative to the phenolate O atom: it is much smaller for the NO2 groups para to the C—O− group [15.23 (9)and 3.92 (14)°] than for the groups in the ortho positions [28.76 (13)–39.84 (11)°].
PMCID: PMC3051773  PMID: 21523064
22.  (1RS,6SR)-Ethyl 4,6-bis­(4-fluoro­phen­yl)-2-oxocyclo­hex-3-ene-1-carboxyl­ate 
In the crystal structure of the title compound, C21H18F2O3, the cyclo­hexene ring has a slightly distorted sofa conformation; the two benzene rings are inclined by 76.27 (8)° and their planes make dihedral angles of 16.65 (10) and 67.53 (7)° with the approximately planar part of the cyclo­hexenone ring [maximum deviation 0.044 (2) Å, while the sixth atom is displaced by 0.648 (3) Å from this plane]. In the crystal, weak inter­molecular C—H⋯O, C—H⋯F and C—H⋯π inter­actions join mol­ecules into a three-dimensional structure.
PMCID: PMC3051537  PMID: 21523019
23.  (1RS,6SR)-Ethyl 4-(4-chloro­phen­yl)-6-(4-fluoro­phen­yl)-2-oxocyclo­hex-3-ene-1-carboxyl­ate toluene hemisolvate 
In the crystal structure of the title compound, C21H18ClFO3·0.5C7H8, the toluene solvent mol­ecules occupy special positions on centres of symmetry, and consequently are disordered across this site. The cyclo­hexene ring has a slightly distorted sofa conformation; the two benzene rings are inclined by 72.90 (7)° and their planes make dihedral angles of 30.09 (10) (chloro­phen­yl) and 88.13 (6)° (fluoro­phen­yl) with the approximately planar part of the cyclo­hexenone ring [maximum deviation from plane through five atoms is 0.030 (2) Å, the sixth atom is 0.672 (3)Å out of this plane]. Weak inter­molecular C—H⋯O and C—H⋯X (X = F, Cl) inter­actions join mol­ecules into a three-dimensional structure. Also, a relatively short and directional C—Cl⋯F—C contact is observed [Cl⋯F = 3.119 (2) Å, C—Cl⋯F = 157.5 (2)° and C—F⋯Cl 108.3 (2)°]. The solvent mol­ecules fill the voids in the crystal structure and are kept there by relatively short and directional C—H⋯π inter­actions.
PMCID: PMC3051615  PMID: 21523018
24.  Disordered structure of propane-1,2-diaminium dichloride 
In the title compound, C3H12N2 2+·2Cl−, the cations are disordered over two well resolved positions in a 0.525 (13):0.475 (13) ratio. The disorder involves two C atoms which assume positions that make an almost mirror-sym­metrical system. Similar disorder is observed both at room temperature and at 120 (1) K. The conformation of the NCCN chain in both components is close to trans (the torsion angles ca ±170°), while that of CCCN chain is close to gauche (±50°). In the crystal, a network of relatively strong N—H⋯Cl hydrogen bonds connects the cations and anions into one-cation-deep layers parallel to (001); there are R 2 4(8) and R 2 4(11) ring motifs within the plane. The planes are only loosely connected by van der Waals contacts and electrostatic inter­actions between cations and anions.
PMCID: PMC3051629  PMID: 21523049
25.  2-Methyl­imidazolium picrate 
In both ionic components of the title salt, C4H7N2 +·C6H2N3O7 −, the rings are approximately planar; the maximum deviation from the mean plane is an order of magnitude larger in the picrate ring [0.0289 (10) Å] than in the imidazolium ring [0.0028 (10) Å. The nitro groups are twisted with respect to the six-atom ring plane; the NO2 groups next to the oxide O atom, at the 2- and 6-positions, are twisted more [by 53.59 (9) and 18.46 (12)°] than the NO2 group at the 4-postition, for which the twist angle is 7.28 (16)°. In the crystal, N—H⋯O hydrogen bonds, in which the hydroxyl O atom acts as a double acceptor and one of the O atoms from a nitro group acts as an additional acceptor, connect mol­ecules into chains along the c-axis direction. Relatively short C—H⋯O contacts and π–π inter­actions between symmetry-related six-membered rings [centroid–centroid distances = 3.5938 (10) and 3.6223 (10) Å] also occur.
PMCID: PMC3050384  PMID: 21522735

Results 1-25 (52)