Tris(2-methoxy-5-bromophenyl)antimony bis(2-nitrobenzoate): Synthesis and specific features of the structure

Tris(5-bromo-2-methoxyphenyl)antimony bis(2-nitrobenzoate) (I) is synthesized by the reaction of tris(5-bromo-2-methoxyphenyl)antimony with 2-nitrobenzoic acid in the presence of hydrogen peroxide (mole ratio 1: 2: 1). According to the X-ray diffraction data, the antimony atom has distorted trigonal bipyramidal coordination. The axial angle OSbO is 177.92(11)°, equatorial bonds CSbC are 109.23(16)°–128.31(16)°, and the Sb-O and Sb-C bond lengths are 2.095(3)–2.125(3) and 2.098(4)–2.113(4) Å, respectively. A specific feature of the structure of complex I is the presence of intramolecular contacts Sb...O(CH₃) (2.992–3.175 Å along with the interactions Sb...O=C (3.039–3.117 Å). The structural organization in crystal is due to weak hydrogen bonds N-O...H-C, C=O...H-C, C-Br...H-C.     

Molecular structure of 3-trifluoroacetamidobenzoyltrifluoroacetone enol form

3-Trifluoroacetamidobenzoyltrifluoroacetone formed in the reaction of 3-aminoacetophenone with an excess of methyl trifluoroacetate crystallizes in the cis-enol form with a hydroxy group located at the carbon atom bound with the trifluoromethyl substituent. Analysis of geometric characteristics indicate the presence of both intramolecular hydrogen bond in the enol fragment and intermolecular H...O contacts in the crystal of the compound.     

A structural systematic study of three isomers of difluoro‐N‐(4‐pyridyl)benzamide

The isomers 2,3‐, (I), 2,4‐, (II), and 2,5‐difluoro‐N‐(4‐pyridyl)benzamide, (III), all with formula C₁₂H₈F₂N₂O, all exhibit intramolecular C—H...O=C and N—H...F contacts [both with S(6) motifs]. In (I), intermolecular N—H...O=C interactions form one‐dimensional chains along [010] [N...O = 3.0181 (16) Å], with weaker C—H...N interactions linking the chains into sheets parallel to the [001] plane, further linked into pairs via C—H...F contacts about inversion centres; a three‐dimensional herring‐bone network forms via C—H...π(py) (py is pyridyl) interactions. In (II), weak aromatic C—H...N(py) interactions form one‐dimensional zigzag chains along [001]; no other interactions with H...N/O/F < 2.50 Å are present, apart from long N/C—H...O=C and C—H...F contacts. In (III), N—H...N(py) interactions form one‐dimensional zigzag chains [as C(6) chains] along [010] augmented by a myriad of weak C—H...π(arene) and O=C...O=C interactions and C—H...O/N/F contacts. Compound (III) is isomorphous with the parent N‐(4‐pyridyl)benzamide [Noveron, Lah, Del Sesto, Arif, Miller & Stang (2002). J. Am. Chem. Soc. 124 , 6613–6625] and the three 2/3/4‐fluoro‐N‐(4‐pyridyl)benzamides [Donnelly, Gallagher & Lough (2008). Acta Cryst. C 64 , o335–o340]. The study expands our series of fluoro(pyridyl)benzamides and augments our understanding of the competition between strong hydrogen‐bond formation and weaker influences on crystal packing.     

Br...O contacts and π–π stacking dominate the packing in methyl 4‐bromo‐3,5‐dimethoxybenzoate

The title compound, C₁₀H₁₁BrO₄, a useful precursor to pharmaceutically active isocoumarin and isochroman derivatives, crystallizes with two unique molecules in the asymmetric unit. A π–π stacking interaction links the planar molecules in the asymmetric unit. Additional π–π contacts stack pairs of molecules along the c axis. A feature of the crystal packing is the presence of a number of short Br...O contacts. A particularly unusual arrangement involves the formation of dimers, with pairs of Br...O contacts imposing a close Br...Br interaction and generating five‐membered rings within an eight‐membered ring formed by two Br...O contacts. Only two comparable arrangements have been reported previously. The Br...O contacts combine with weak C—H...O hydrogen bonds to form corrugated sheets of molecules approximately parallel to (001). These sheets are stacked along the c axis by π–π interactions to generate a three‐dimensional network.     

Polymorphic form IV of olanzapine

2‐Methyl‐4‐(4‐methylpiperazin‐1‐yl)‐10H‐thieno[2,3‐b][1,5]benzodiazepine, C₁₇H₂₀N₄S, commonly known as olanzapine, is a psychotropic agent that belongs to the thienobenzodiazepine class of drugs. A new polymorph form IV was obtained upon attempted cocrystallization with nicotinamide in a 1:1 ratio from an ethyl acetate solution. Two butterfly‐like molecules form centrosymmetric dimers stabilized by weak C—H...π interactions between the 4‐methylpiperazin‐1‐yl fragment and the benzene/thiophene aromatic system. Form IV consists of a herringbone arrangement of dimers, whereas the previously reported form II has parallel dimers. Both crystal structures are sustained by an N—H...N hydrogen bond.     

Critical Molecular Coordination Numbers in the Structural Class P21/c,Z = 4(1)

Moscow University Chemistry Bulletin - The network of intermolecular contacts in an organic crystal contains a finite set of strong contacts sufficient to form a network. These contacts form a...     

Halobenzenes and Ir(I): kinetic C-H oxidative addition and thermodynamic C-Hal oxidative addition

A (PNP)Ir fragment undergoes facile, room-temperature oxidative addition of C-H bonds in arenes and haloarenes in preference to aromatic carbon-halogen bonds. This preference, however, is determined to be kinetic in nature. Oxidative addition of C-Cl and C-Br is preferred thermodynamically. The products of the C-Cl or C-Br oxidative addition are separated from the C-H oxidative addition products by a high activation barrier and are only accessible at >100 degrees C. Of the C-H oxidative addition products of chlorobenzene, the isomer with the o-ClC6H4 ligand has the lowest energy.     

Platinum stilbazoles: ring-walking coupled with aryl-halide bond activation

The reaction between tetrakis(triethylphosphine)platinum(0) and 4-[trans-2-(4-bromophenyl)vinyl]pyridine (1) is examined. Initially, the metal center coordinates to the bridging double bond of 1. Complexes 2 and 3 were fully characterized, and their X-ray crystallography structures are presented. Upon heating, either in solution or in the solid state, complex 2 undergoes C-Br oxidative addition to give complex 3. Kinetic studies revealed that this conversion is unimolecular and does not involve dissociation of the metal center from the double bond. Density functional studies show that a plausible mechanism involves the metal center "walking" around the pi-system from the bridging C=C double bond to the C-Br bond.     

Combined nonadiabatic transition-state theory and ab initio molecular dynamics study on selectivity of the alpha and beta bond fissions in photodissociation of bromoacetyl chloride

The selectivity of the alpha C-Cl and beta C-Br bond fissions upon n-->pi(*) excitation of bromoacetyl chloride has been investigated with combined nonadiabatic Rice-Ramsperger-Kassel-Marcus theory and ab initio molecular dynamics calculations, which are based on the potential energy profiles calculated with the complete active space self-consistent field and multireference configuration interaction methods. The Zhu-Nakamura [J. Chem. Phys. 101, 10630 (1994); 102, 7448 (1995)] theory is chosen to calculate the nonadiabatic hopping probability. It is found that nonadiabatic effect plays an important role in determining selective dissociations of the C-Cl and C-Br bonds. The calculated rate constants are close to those from experimentally inferred values, but the branching ratio of the alpha C-Cl and beta C-Br bond fissions is different from the experimental findings. The direct molecular dynamics calculations predict that fission of the C-Cl bond occurs on a time scale of picoseconds and cleavage of the beta C-Br bond proceeds with less probability within the same period. This reveals that the initial relaxation dynamics is probably another important factor that influences the selectivity of the C-Cl and C-Br bond fissions in photodissociation of BrCH(2)COCl at 248 nm.     

Strength of Calpha-H...O=C hydrogen bonds in transmembrane proteins

A large number of Calpha-H...O contacts are present in transmembrane protein structures, but contribution of such interactions to protein stability is still not well understood. According to previous ab initio quantum calculations, the stabilization energy of a Calpha-H...O contact is about 2-3 kcal/mol. However, experimental studies on two different Calpha-H...O hydrogen bonds present in transmembrane proteins lead to conclusions that one contact is only weakly stabilizing and the other is not even stabilizing. We note that most previous computational studies were on optimized geometries of isolated molecules, but the experimental measurements were on those in the structural context of transmembrane proteins. In the present study, 263 Calpha-H...O=C contacts in alpha-helical transmembrane proteins were extracted from X-ray crystal structures, and interaction energies were calculated with quantum mechanical methods. The average stabilization energy of a Calpha-H...O=C interaction was computed to be 1.4 kcal/mol. About 13% of contacts were stabilizing by more than 3 kcal/mol, and about 11% were destabilizing. Analysis of the relationships between energy and structure revealed four interaction patterns: three types of attractive cases in which additional Calpha-H...O or N-H...O contact is present and a type of repulsive case in which repulsion between two carbonyl oxygen atoms occur. Contribution of Calpha-H...O=C contacts to protein stability is roughly estimated to be greater than 5 kcal/mol per helix pair for about 16% of transmembrane helices but for only 3% of soluble protein helices. The contribution would be larger if Calpha-H...O contacts involving side chain oxygen were also considered.     

Nonadiabatic effects in C-Br bond scission in the photodissociation of bromoacetyl chloride

Bromoacetyl chloride photodissociation has been interpreted as a paradigmatic example of a process in which nonadiabatic effects play a major role. In molecular beam experiments by Butler and co-workers [J. Chem. Phys. 95, 3848 (1991); J. Chem. Phys. 97, 355 (1992)], BrCH2C(O)Cl was prepared in its ground electronic state (S0) and excited with a laser at 248 nm to its first excited singlet state (S1). The two main ensuing photoreactions are the ruptures of the C-Cl bond and of the C-Br bond. A nonadiabatic model was proposed in which the C-Br scission is strongly suppressed due to nonadiabatic recrossing at the barrier formed by the avoided crossing between the S1 and S2 states. Recent reduced-dimensional dynamical studies lend support to this model. However, another interpretation that has been given for the experimental results is that the reduced probability of C-Br scission is a consequence of incomplete intramolecular energy redistribution. To provide further insight into this problem, we have studied the energetically lowest six singlet electronic states of bromoacetyl chloride by using an ab initio multiconfigurational perturbative electronic structure method. Stationary points (minima and saddle points) and minimum energy paths have been characterized on the S0 and S1 potential energy surfaces. The fourfold way diabatization method has been applied to transform five adiabatic excited electronic states to a diabatic representation. The diabatic potential energy matrix of the first five excited singlet states has been constructed along several cuts of the potential energy hypersurfaces. The thermochemistry of the photodissociation reactions and a comparison with experimental translational energy distributions strongly suggest that nonadiabatic effects dominate the C-Br scission, but that the reaction proceeds along the energetically allowed diabatic pathway to excited-state products instead of being nonadiabatically suppressed. This conclusion is also supported by the low values of the diabatic couplings on the C-Br scission reaction path. The methodology established in the present study will be used for the construction of global potential energy surfaces suitable for multidimensional dynamics simulations to test these preliminary interpretations.     

Stoichiometric and catalytic activation of the alpha- and beta-2,3,4-tri-O-acetyl-5-thioxylopyranosyl bromide inside the cavity of the Pd3(dppm)3(CO)2+ cluster

The title cluster (Pd(3)(2+)) exhibits a pronounced affinity for Br(-) ions to form the very stable Pd(3)(Br)(+) adduct. Upon a 2-electron reduction, a dissociative process occurs generating Pd(3)(0) and eliminating Br(-) according to an ECE mechanism (electrochemical, chemical, electrochemical). At a lower temperature (i.e. -20 degrees C), both ECE and EEC processes operate. This cluster also activates the C-Br bond, and this work deals with the reactivity of Pd(3)(2+) with 2,3,4-tri-O-acetyl-5-thioxylopyranosyl bromide (Xyl-Br), both alpha- and beta-isomers. The observed inorganic product is Pd(3)(Br)(+) again, and it is formed according to an associative mechanism involving Pd(3)(2+).Xyl-Br host-guest assemblies. In an attempt to render the C-Br bond activation catalytic, these species are investigated under reduction conditions at two potentials (-0.9 and -1.25 V vs SCE). In the former case, the major product is Xyl-H, issued from a radical intermediate Xyl(*) abstracting an H atom from the solvent. Evidence for Xyl(*) is provided by the trapping with TEMPO (2,2,6,6-tetramethyl-1-piperidinyloxy) and DMPO (5,5'-dimethylpyrroline-N-oxyde). In the second case, only one product is observed, 3,4-di-O-acetyl-5-thioxylal, which is issued from the Xyl(-)() intermediate anion.     

C–H...O and C–H...N interactions in RNA structures

Small molecule studies indicate that C–H...X interactions (X: O,N) constitute weak H-bonds. We have performed a comprehensive analysis of their occurrence and geometry in RNA structures. Here, we report on statistical properties of the total set of interactions identified and discuss selected motifs. The distance/angle distribution of all interactions exhibits an excluded region where the allowed C–H...X angle range increases with an increasing H...X distance. The preferred short C–H...X interactions in RNA are backbone-backbone contacts between neighbour nucleotides. Distance/angle distributions generated for various interaction types can be used for error recognition and modelling. The axial C2′(H)...O4′ and C5′(H)...O2′ interactions connect two backbone segments and form a seven-membered ring that is specific for RNA. An AA base pair with one standard H-bond and one C–H...N interaction has been identified in various structures. Despite the occurrence of short C–H...X contacts their free energy contribution to RNA stability remains to be assessed. Received: 17 May 1998 / Accepted: 4 August 1998 / Published online: 2 November 1998     

Conformation versus coordination: synthesis and structural investigations of tellurium(II) dithiolates derived from beta-donor-substituted thiols

New methods of preparing tellurium(II) dithiolates, Te(SR)(2), are presented. Te(SCH(2)CH(2)OAc)(2), 1, was made from Te(SCH(2)CH(2)OH)(2) by acetylation of the hydroxyl groups. Te(SCH(2)CH(2)SAc)(2), 2, [Te(SCH(2)CH(2)NH(3))(2)]Cl(2), 3, and Te(SC(6)H(4)(o-NH(2)))(2), 4, were synthesized by ligand exchange reactions of Te(S(t)Bu)(2) with 2 equiv of HSCH(2)CH(2)SAc, [HSCH(2)CH(2)NH(3)]Cl, and HSC(6)H(4)(o-NH(2)), respectively. Of all compounds, 4 exhibits the strongest thermal sensitivity toward decomposition and the largest low-field shift of the (125)Te NMR signal, two features that are attributed to weak Te.N interactions. The structural parameters of the CSTeSC unit exhibit very similar values for all four compounds, while the torsion angles of the side chains differ between the molecules, a feature rationalized by ab initio studies. In the solid state, different kinds of intermolecular aggregation and contacts to the Te atoms are present. 1 and 2 crystallize in the same space group (orthorhombic, Pbcn) and exhibit C(2) symmetric molecules, with two intermolecular Te.S contacts, leading to a trapezoidal coordination mode of the Te atoms. SCCE and C(S)CEC (with E = O, S) torsion angles represent the major differences between 1 and 2, which are attributed to their unlike intermolecular hydrogen bridges. In the solid state structure of 3, [Te(SCH(2)CH(2)NH(3))(2)](2+) cations and Cl(-) anions form a three-dimensional network via N-H...Cl and C-H...Cl hydrogen bonds (triclinic, P(-)1). Two neighboring [Te(SCH(2)CH(2)NH(3))(2)](2+) cations are linked via two Te...S contacts, and each Te atom forms one additional Te...Cl contact, resulting in a slightly distorted trapezoidal coordination mode. In the solid state structure of 4, adjacent molecules form Te...Te and Te...N contacts as well as hydrogen bridges. Two chemically different Te atoms are present, both of which are tetracoordinate with distorted sawhorse configurations. The absence of intramolecular Te...O, Te...S, or Te...N contacts in 1, 2, and 4, respectively, is attributed to the conformational rigidity of the CSTeS unit, where conformation ruling coordination is the case.     

Nature of weak inter- and intramolecular interactions in crystals. 1. The F...O and F...H contacts in the crystal of 2-trifluoroacetyl-5-trifluoromethylpyrrole

The topological analysis of the electron density distribution in the crystal of 2-trifluoroacetyl-5-trifluoromethylpyrrole revealed that the F...H and F...O intermolecular contacts correspond to attractive interactions. The energies of these interactions were estimated from the experimental data and it was shown that these contacts are similar to the C—H...O contacts. Analysis of the deformation electron density revealed that the F...O contacts correspond to transfer of the lone electron pair of a fluorine atom to the antibonding -orbital of the C=O bond.     

The low‐melting compounds 1,4‐diethyl‐, 1,2‐diethyl‐ and ethylbenzene

Crystals of 1,4‐diethyl‐ and 1,2‐diethylbenzene, both C₁₀H₁₄, and ethylbenzene, C₈H₉, have been grown in situ. The molecules of 1,4‐diethyl‐ and 1,2‐diethylbenzene are located about a centre of inversion and across a twofold axis, respectively. In both molecules, the terminal methyl groups are located on opposite sides of the plane of the aromatic ring. In the crystal structures of all three compounds, molecules are linked together by (Ar)C—H...π and CH₂...π contacts. The methyl H atoms do not form close contacts with any of the aromatic π systems.     

Weak intermolecular interactions in isomorphous 5‐(2‐chloroethoxy)‐2,3‐dihydro‐1,4‐benzodioxine and 5‐(2‐bromoethoxy)‐2,3‐dihydro‐1,4‐benzodioxine: bonding or nonbonding interactions

The title compounds, C₁₀H₁₁ClO₃, (I), and C₁₀H₁₁BrO₃, (II), are isomorphous and effectively isostructural; all of the interatomic distances and angles are normal. The structures exhibit long intermolecular C—H...O and C—H...π contacts with attractive energies ranging from 1.17 to 2.30 kJ mol⁻¹. Weak C—H...O hydrogen bonds form C(3) and C(4) motifs, combining to form a two‐dimensional R₃⁴(12) net. No face‐to‐face stacking interactions are observed.     

Aurophilic interactions in cationic gold complexes with two isocyanide ligands. Polymorphic yellow and colorless forms of [(cyclohexyl isocyanide)2AuI](PF6) with distinct luminescence

Crystallographic studies of yellow and colorless forms of [(C(6)H(11)NC)(2)Au(I)](PF(6)) show that they are polymorphs with differing, but close, contacts between the gold atoms which form extended chains. In the colorless polymorph the gold cations form linear chains with a short Au...Au contact (3.1822(3) A) indicative of an aurophilic attraction. The structure of the yellow polymorph is more complicated with four independent cations forming kinked, slightly helical chains with very short Au...Au contacts of 2.9803(6), 2.9790(6), 2.9651(6), and 2.9643(6) A. However, in the related compound, [(CH(3)NC)(2)Au(I)](PF(6)), each cation is surrounded by six hexafluorophosphate ions and there is no close Au...Au contact despite the fact that the isocyanide ligand has less steric bulk. The crystalline colorless and yellow polymorphs are both luminescent at 298 K, lambda(max): 424 nm (colorless) or 480 nm (yellow). Colorless solutions of the two polymorphs have identical absorption spectra and are nonluminescent at room temperature. Freezing solutions of [(C(6)H(11)NC)(2)Au(I)](PF(6)) produces intense luminescence which varies depending upon the solvent involved. Each polymorph melts to give a colorless but luminescent liquid which reverts to the yellow polymorph upon cooling.     

(1‐Pyridinio)perfluorophenacylide: a new stable pyridinium ylide in the enol form

The title compound, C₁₃H₆F₅NO, exists in the enol form and adopts the E configuration about the enol double bond. It is the first example of an enol‐type pyridinium ylide. The enol structure was unambiguously determined on the basis of the significantly longer C—O bond and shorter C—C bond. Intramolecular C—H...O and C—H...F hydrogen bonds are responsible for promotion of the enol form and for the stability of this compound.