Boron triel bonding: a weak electrostatic interaction lacking electron-density descriptors.

In an effort to describe π-hole interactions, we undertook accurate high-resolution X-ray diffraction analyses of single crystals of 1,4-dinitrobenzene, a co-crystal of cis-tartaric acid and bis-pyridine N-oxide and the hydrochloride of B-4-pyridinylboronic acid. We selected these three compounds owing to the π-hole accessibility features that the sp2 hybridized B, C and N atoms provide, thus allowing us to compare the fundamental characteristics of π-hole interactions using Bader's Atom in Molecules (AIM) theory. This particular study required extremely accurate experimental diffraction data, because the interaction of interest is weak. As shown by the experimental charge density maps of the -YO2 (Y = B, C, N) units, we assign the depletion of electron-density present in the central boron, carbon and nitrogen atoms (electrophilic π-holes) as the main origin for the establishment of intermolecular Lewis acid-Lewis base attractive interaction with complementary electron-rich regions. Unexpectedly, the Bader's analyses of both experimentally and theoretically calculated charge distribution maps for the solid involving the - BO2H2 group do not show the presence of bond paths, neither of the bond critical points, between the interacting electron rich sites and the boron or carbon atoms featuring the electron hole. In contrast, these topological descriptors of chemical interactions for the AIM theory were easily located in the solid-state structures of the compounds involving the carboxylic and the nitro groups.

Joint refinement model for the spin resolved one-electron reduced density matrix of YTiO3 using magnetic structure factors and magnetic Compton profiles data.

In this paper, we propose a simple cluster model with limited basis sets to reproduce the unpaired electron distributions in a YTiO3 ferromagnetic crystal. The spin-resolved one-electron-reduced density matrix is reconstructed simultaneously from theoretical magnetic structure factors and directional magnetic Compton profiles using our joint refinement algorithm. This algorithm is guided by the rescaling of basis functions and the adjustment of the spin population matrix. The resulting spin electron density in both position and momentum spaces from the joint refinement model is in agreement with theoretical and experimental results. Benefits brought from magnetic Compton profiles to the entire spin density matrix are illustrated. We studied the magnetic properties of the YTiO3 crystal along the Ti-O1-Ti bonding. We found that the basis functions are mostly rescaled by means of magnetic Compton profiles, while the molecular occupation numbers are mainly modified by the magnetic structure factors.

Synthesis, structure and Hirshfeld surface analysis of 2-oxo-2H-chromen-6-yl 4-tert-butyl-benzoate: work carried out as part of the AFRAMED project.

In the title compound, C20H18O4, the dihedral angle between the 2H-chromen-2-one ring system and the phenyl ring is 89.12 (5)°. In the crystal, the mol-ecules are connected through C-H⋯O hydrogen bonds to generate [010] double chains that are reinforced by weak aromatic π-π stacking inter-actions. The unit-cell packing can be described as a tilted herringbone motif. The H⋯H, H⋯O/O⋯H, H⋯C/C⋯H and C⋯C contacts contribute 46.7, 24.2, 16.7 and 7.6%, respectively, to its Hirshfeld surface.

Experimental and theoretical charge density analysis of a bromoethyl sulfonium salt.

Bromoethyl sulfonium trifluoromethanesulfonate is a salt complex in which a sulfur atom makes three covalent bonds. This molecule has been proved to act as an efficient annulation reagent which results in formation of synthetically challenging and pharmaceutically important 4-, 5-, 6-, and 7-membered heterocycles in excellent yields. The charge density of the molecule was determined from both experimentally and theoretically derived diffraction data. The stereochemistry and electron density topology of the sulfonium group was analyzed. To understand the chemical reactivity of the molecule, the electrostatic potential difference between the two carbon atoms of the bromoethyl group was investigated. It has been considered that the hydrogen atoms on the carbon atom bound to sulfur are more acidic in character due to their vicinity with the triply covalently bonded positively charged sulfur atom. The electropositivity of the S-attached and Br-attached methylene groups are compared in the experimental and theoretical charge densities using topological atomic charges and electrostatic potential at the molecular surface.

Poly[di-µ-aqua-di-aqua-bis-(µ7-oxalato-κ(9) O (1):O (1):O (1),O (2):O (2):O (2'):O (2'),O (1'):O (1'))calciumdicaesium].

In the title compound, [CaCs2(C2O4)2(H2O)4] n , the Ca(2+) ion, lying on a twofold rotation axis, is coordinated by four O atoms from two oxalate ligands and two bridging water mol-ecules in an octa-hedral geometry. The Cs(+) ion is coordinated by seven O atoms from six oxalate ligands, one bridging water and one terminal water mol-ecule. The oxalate ligand displays a scarce high denticity. The structure contains parallel chain units runnig along [10-1], formed by two edge-sharing Cs polyhedra connected by CsO9 polyhedra connected by a face-sharing CaO6 octahedron. These chains are further linked by the oxalate ligands to build up a three-dimensional framework. O-H⋯O hydrogen bonds involving the water mol-ecules and the carboxyl-ate O atoms enhance the extended structure.

Synthesis, crystal structure and phase transitions of novel hybrid perovskite: bis(1,2-diaminopropane) di-µ-chloro-bis[diaquadichloromanganate(II)] dichloride.

Single crystals of bis(1,2-diaminepropane) di-µ-chloro-bis[diaquadichloromanganate(II)] dichloride have been prepared by evaporation from ethanoic solution. The triclinic X-ray crystal structure is built as layers of centrosymmetric dimers of [Mn(Cl)4(H2O)2]2- octahedra and 1,2-diaminopropane. The inorganic part consists of Mn octahedra sharing one edge and distributed in the basal ac plane along the a direction. These doubly negative charged layers are separated along the b axis by a positively charged diamine propane layer. One Cl- anion contributes to the electroneutrality of the crystal interacting with both inorganic - through a hydrogen bond network to the two water molecules coordinated to Mn - and organic layers via the NH3+ ammonium group. Differential scanning calorimetry shows two endothermic main peaks at T = 366 K and T = 375 K related to the release of the water molecules. The resulting dehydrated material is C-centered monoclinic as shown by powder X-ray diffraction.

Can a formally zwitterionic rhodium(I) complex emulate the charge density of a cationic rhodium(I) complex? A combined synchrotron X-ray and theoretical charge-density study.

The molecular electron densities of structurally related cationic ([(κ(2)-3-P(i)Pr(2)-2-NMe(2)-indene)Rh(COD)](CF(3)SO(3)), [1c](CF(3)SO(3))) and formally zwitterionic ([(κ(2)-3-P(i)Pr(2)-2-NMe(2)-indenide)Rh(COD)], 1z) complexes were accurately determined using synchrotron bright-source X-ray radiation at 30 K followed by multipolar refinement (COD = η(4)-1,5-cyclooctadiene). The densities were also obtained from density functional theory calculations with a large, locally dense basis set. A 28-electron ([Ar]3d(10)) core of the Rh atom was modeled by an effective core potential to obtain a density that was then augmented with relativistic cores according to the Keith-Frisch approximation. Calculations were performed at the experimental geometry and after vacuum-phase geometry optimization starting from the experimental geometry. Experimental and calculated geometries and electron-density distributions show that the electron density and electronic structure in the region of the Rh center are not significantly altered by protonation of the aromatic ring and that formal removal of CF(3)SO(3)H from [1c](CF(3)SO(3)) affords a complex 1z possessing substantial zwitterionic character (with a charge separation of ca. 0.9 electronic charge) featuring a negatively charged aromatic indenide framework. Further, the molecular electrostatic potentials of 1c and 1z exhibit similar topography around the metal, despite being drastically different in the vicinity of the indene or indenide portion of the cation (1c) and zwitterion (1z), respectively. Collectively, these observations obtained from high-level experimental and theoretical electron-density analysis confirm, for the first time, that appropriately designed zwitterionic complexes can effectively emulate the charge distribution found within ubiquitous cationic platinum-group metal catalyst complexes, in keeping with recent catalytic investigations.

Experimental and database-transferred electron-density analysis and evaluation of electrostatic forces in coumarin-102 dye.

The electron-density distribution of a new crystal form of coumarin-102, a laser dye, has been investigated using the Hansen-Coppens multipolar atom model. The charge density was refined versus high-resolution X-ray diffraction data collected at 100 K and was also constructed by transferring the charge density from the Experimental Library of Multipolar Atom Model (ELMAM2). The topology of the refined charge density has been analysed within the Bader `Atoms In Molecules' theory framework. Deformation electron-density peak heights and topological features indicate that the chromen-2-one ring system has a delocalized π-electron cloud in resonance with the N (amino) atom. The molecular electrostatic potential was estimated from both experimental and transferred multipolar models; it reveals an asymmetric character of the charge distribution across the molecule. This polarization effect is due to a substantial charge delocalization within the molecule. The molecular dipole moments derived from the experimental and transferred multipolar models are also compared with the liquid and gas-phase dipole moments. The substantial molecular dipole moment enhancements observed in the crystal environment originate from the crystal field and from intermolecular charge transfer induced and controlled by C-H···O and C-H···N intermolecular hydrogen bonds. The atomic forces were integrated over the atomic basins and compared for the two electron-density models.

l-Leucinium fluoride monohydrate.

The asymmetric unit of the title hydrated salt, C(6)H(14)NO(2) (+)·F(-)·H(2)O, contains a discrete cation with a protonated amino group, a halide anion and one water mol-ecule. The crystal structure is composed of double layers parallel to (010) held together by N-H⋯O, N-H⋯F, O-H⋯F and C-H⋯F hydrogen bonds, forming a two-dimensional network, and stacked along the c axis, viz. hydro-philic layers at z = 0 and 1/2 and hydro-phobic layers at z = 1/3 and 2/3.

dl-Tyrosinium chloride dihydrate.

In the title compound, C(9)H(12)NO(3) (+)·Cl(-)·2H(2)O, the cation has a protonated amino group resulting from proton transfer from chloridric acid. The structure displays double layers parallel to the [010] direction held together by N-H⋯O, N-H⋯Cl, O-H⋯O and O-H⋯Cl hydrogen bonds. These layers are stacked along the c axis at b = 1/2; within each layer, the tyrosinium cations are arranged in an alternating head-to-tail sequence, forming inversion dimers [R(2) (2)(10) motif]. The water mol-ecules allow for the construction of a three-dimensional hydrogen-bonded network formed by centrosymmetric R(6) (6)(28) and R(8) (8)(34) motifs.

Bis(adeninium) bis-(hydrogensulfate) sulfate.

The title compound, 2C5H7N5(2+)·2HSO4(-)·SO4(2-), was synthesized from adenine and sulfuric acid. The asymmetric unit contains two diprotonated adeninium cations, two bis-ulfate anions and one sulfate anion. The crystal structure is stabilized by classical N-H⋯O and O-H⋯O hydrogen bonds, and weak C-H⋯O and C-H⋯N hydrogen bonds, generating a three-dimensional network.

Intra- and supra-molecular inter-actions in cis,mer-diaqua-tris-(1H-imidazole-κN(3))(terephthalato-κO)cobalt(II) monohydrate.

In the title compound, [Co(C(8)H(4)O(4))(C(3)H(4)N(2))(3)(H(2)O)(2)]·H(2)O, the cisoid angles are in the range 85.59 (5)-93.56 (5)°, while two equal transoid angles deviate significantly from the ideal linear angle, the third being almost linear. One carboxyl-ate group is almost coplanar [1.23 (13)°] with the plane of its parent aromatic ring, although it has one O-atom donor involved in one coordination and one hydrogen bond as acceptor. The other carboxyl-ate group does not coordinate and is rotated out of this plane with a torsional twist of 17.27 (20)°. The coordination neutral entity, based on aqua ligands and two cyclic co-ligands seems, at first sight, monomeric. Strongly tight, via one intra-molecular hydrogen bond between aqua and carboxyl-ate O atoms, it brings out a quasi-planar six-membered ring around the Co(II) atom, turning the CoN(3)O(3) coordination octa-hedron into a new building block. The rigidity of this feature associated with several hydrogen-bonded arrays yields an extended structure. In the resulting supra-molecular packing, a binuclear hydrated Co(II) assembly, built up from triple strands driven by different heterosynthons, embodies the synergy of coordination, covalent and hydrogen bonds.

Topological analysis of hydrogen bonds and weak interactions in protein helices via transferred experimental charge density parameters.

Helices represent the most abundant secondary structure motif in proteins and are often involved in various functional roles. They are stabilized by a network of hydrogen bonds between main chain carbonyl and amide groups. Several surveys scrutinized these hydrogen bonds, mostly based on the geometry of the interaction. Alternatively, the topological analysis of the electron density provides a powerful technique to investigate hydrogen bonds. For the first time, transferred experimental charge density parameters (ELMAM database) were used to carry out a topological analysis of the electron density in protein helices. New parameters for the description of the hydrogen bond geometry are proposed. Bonding contacts between the amide N and carbonyl O atoms (N···O) of helices, poorly addressed in the literature so far, were characterized from topological, geometrical, and local energetic analyses. Particularly, a geometrical criterion allowing for the discrimination between hydrogen bonds and N···O contacts is proposed.

Charge density analysis of 2-methyl-4-nitro-1-phenyl-1H-imidazole-5-carbonitrile: an experimental and theoretical study of C≡N···C≡N interactions.

The experimental charge density distribution was determined for 2-methyl-4-nitro-1-phenyl-1H-imidazole-5-carbonitryle, using the Hansen-Coppens multipole model. Free R factor calculations were performed with MoPro software to find optimal restraints for a physically meaningful model. The crystal packing is determined to some extent by weak C-H···O and C-H···N hydrogen bonds but mostly by a lateral electrostatic interaction between antiparallel side-by-side C≡N groups. Electrostatic energy calculations were performed based on the experimental data and are in line with the high-level, explicitly correlated theoretical SCS-RI-MP2-F12 calculations of total energy. The molecular dipole moment and atomic charge values were compared for different experimental and theoretical models, to highlight the dependence of the electrostatic property outputs on the applied restraints. Interesting O···O contacts are also described. The results are compared with two recently investigated nitroimidazole derivatives, namely, 1-(2'-aminophenyl)-2-methyl-4-nitroimidazole and 1-phenyl-4-nitroimidazole.

Intermolecular interactions and charge transfer in the 2:1 tetrathiafulvalene bromanil complex, (TTF)2-BA.

The crystal structure of the 2:1 charge-transfer complex of tetrathiafulvalene [2,2'-bis(1,3-dithiolylidene)] and bromanil (tetrabromo-1,4-benzoquinone) [(TTF)(2)-BA, (C(6)H(4)S(4))(2)-C(6)Br(4)O(2)] has been determined by X-ray diffraction at room temperature, 100 and 25 K. No structural phase transition occurs in the temperature range studied. The crystal is made of TTF-BA-TTF sandwich trimers. A charge-transfer estimation between donor and acceptor (0.2 e) molecules is proposed in comparison to the molecular geometries of TTF-BA and TTF and BA isolated molecules. Displacement parameters of the molecules have been modeled with the TLS formalism.

R-free factor and experimental charge-density analysis of 1-(2'-aminophenyl)-2-methyl-4-nitroimidazole: a crystal structure with Z' = 2.

The experimental charge-density distribution was determined for 1-(2'-aminophenyl)-2-methyl-4-nitro-1H-imidazole crystals. An anharmonic model was applied to the N atoms of both amino groups and to one nitro group in order to account for high residual peaks after harmonic multipole refinement and to obtain a better charge-density model. Free R-factor calculations [Brünger (1992). Nature, 355, 472-475] with restrained models implemented in MoPro were used to determine the degree of similarity of the two symmetry-independent molecules in the unit cell. The results are compared with 1-phenyl-4-nitroimidazole in order to analyze the influence of the amine and methyl functional groups. The asymmetric unit contains two symmetry-independent molecules giving rise to a dimer connected via strong N-H···N hydrogen bonds; these dimers are the building blocks of the crystal. In the crystal structure there are also weaker interactions and many short directional contacts (C-H···O, C-H···N and C-H···π), for which the Koch-Popelier topological criteria were applied. This analysis revealed that the C-H···π interactions lie at the border between weak hydrogen bonds and van der Waals interactions. Special attention was also paid to stabilizing H···H interactions. It turned out that the electron density, Laplacian and density energies at the critical points show an exponential dependence on the contact distance, similar to the relation found for other interactions.

d-Orbital orientation in a dimer cobalt complex: link to magnetic properties?

The experimental charge-density distribution of the dinuclear cobalt(II) complex [Co(2)(sym-hmp)(2)](BPh(4))(2)·2H(2)O·2C(3)H(6)O was determined at 100 K. When decreasing the temperature, the magnetic susceptibility of this complex deviates from Curie law because of anti-ferromagnetic exchange interactions, but the susceptibility increases sharply at low temperature (< 20 K). To explain this magnetic behaviour a tilt angle between the Co-atom environments was previously theoretically predicted. The structure and experimental charge density determined in this study show a tilt angle. The calculated value, based on the 100 K experimental d-orbital model, is in agreement with the theoretical one.

Poly[diaquadi-µ6-oxalato-µ5-oxalato-chromium(III)rubidium(I)]: a new supramolecular isomer.

The title compound, [CrRb(C(2)O(4))(2)(H(2)O)(2)](n), obtained under hydrothermal conditions and investigated structurally at 100 K, is a three-dimensional supramolecular isomer of the layered structure compound studied at room temperature. This novel polymer is built up from crosslinked heterobimetallic units. The linkage of alternating edge- and vertex-shared RbO(7)(H(2)O)(2) and CrO(4)(H(2)O)(2) polyhedra running along three different directions gives a dense packing. The two independent ligands display two η(4)-chelation modes and two conventional carboxylate bridges. However, the pentadentate ligand connects the Cr(III) and Rb(I) ions through one O-atom bridge, while the hexadentate ligand exhibits an additional η(3)-chelation and two O-atom bridges. Each coordinated water molecule forms an O-atom bridge between the two metals. Moreover, in the absence of protonated ligands, these water molecules act as donors through their four H atoms in strong-to-weak hydrogen bonds. This results in zigzag chains of alternating oxalate and aqua ligands parallel to the twofold screw axis. The six double oxalates known to date containing an alkali and Cr(III) all present layered two-dimensional structures. In the series, this supramolecular isomer is the first three-dimensional framework.

Spin-resolved atomic orbital model refinement for combined charge and spin density analysis: application to the YTiO3 perovskite.

A new crystallographic method is proposed in order to refine a spin-resolved atomic orbital model against X-ray and polarized neutron diffraction data. This atomic orbital model is applied to the YTiO3 perovskite crystal, where orbital ordering has previously been observed by several techniques: X-ray diffraction, polarized neutron diffraction and nuclear magnetic resonance. This method gives the radial extension, orientation and population of outer atomic orbitals for each atom. The interaction term between Ti3+, Y3+ cations and O2- ligands has been estimated. The refinement statistics obtained by means of the orbital method are compared with those obtained by the multipole model previously published.

Synthesis of polyhalogenated 4,4'-bipyridines via a simple dimerization procedure.

Polyhalogenated 4,4'-bipyridines were conveniently synthesized in a single step starting from dihalopyridines. A mechanism was proposed on the basis of experiments performed with 2-chloro-5-bromopyridine 1a. 2-Chloro-4-lithio-5-bromopyridine A1 was produced via ortholithiation of 1a by using either LDA or t-BuLi bases. When LDA was used, dimer 3a containing two chlorines and two bromine atoms was formed predominantly accompanied by several byproducts whose structure and mechanism of formation are discussed. In the case of t-BuLi, although the major product was 2-chloropyridine 7, a new pyridone product 8 was formed that is probably the result of the dihydropyridine intermediate hydrolysis. The dimerization procedure involving LDA was employed to prepare a large number of halogenated 4,4'-bipyridines in moderate to good yields. In some specific cases, halogenated 3,4' and 2,4'-bipyridines were obtained in lower yields and their structures were unambiguously assigned by X-ray diffraction analysis.