Parallel Water/Aromatic Interactions of Non‐Coordinated and Coordinated Water

The parallel interactions of non‐coordinated and coordinated water molecules with an aromatic ring were studied by analyzing data in the Cambridge structural database (CSD) and by using quantum chemical calculations. The CSD data show that water/aromatic contacts prefer parallel to OH/π interactions, which indicates the importance of parallel interactions. The results reveal the influence of water coordination to a metal ion; the interactions of aqua complexes are stronger. Coordinated water molecules prefer a parallel‐down orientation in which one O?H bond is parallel to the aromatic ring, whereas the other O?H bond points to the plane of the ring. The interactions of aqua complexes with parallel‐down water/benzene orientation are as strong as the much better known OH/π orientations. The strongest calculated interaction energy is ?14.89 kcal mol^?1. The large number of parallel contacts in crystal structures and the quite strong interactions indicate the importance of parallel orientation in water/benzene interactions.     

Nature of the water/aromatic parallel alignment interactions

The water/aromatic parallel alignment interactions are interactions where the water molecule or one of its O? H bonds is parallel to the aromatic ring plane. The calculated energies of the interactions are significant, up to ΔE_{CCSD(T)(limit)} = ?2.45 kcal mol^?1 at large horizontal displacement, out of benzene ring and CH bond region. These interactions are stronger than CH···O water/benzene interactions, but weaker than OH···π interactions. To investigate the nature of water/aromatic parallel alignment interactions, energy decomposition methods, symmetry‐adapted perturbation theory, and extended transition state‐natural orbitals for chemical valence (NOCV), were used. The calculations have shown that, for the complexes at large horizontal displacements, major contribution to interaction energy comes from electrostatic interactions between monomers, and for the complexes at small horizontal displacements, dispersion interactions are dominant binding force. The NOCV‐based analysis has shown that in structures with strong interaction energies charge transfer of the type π → σ*(O? H) between the monomers also exists. © 2014 Wiley Periodicals, Inc.     

Synthesis and Crystal Structure of a [Mo8O26]4– Cluster Derivative with 4‐MePyH+. First β‐Octamolybdate Derivative with π–π Stacking

Dioxobis(pyridine‐2‐thiolate‐N, S)molybdenum(VI) (MoO₂(Py‐S)₂), reacts with of 4‐methylpyridine (4‐MePy) in acetonitrile, by slow diffusion, to afford the title compound. This has been characterized by elemental analysis, IR and ¹H NMR spectroscopy. The X‐ray single crystal structure of the complex is described. Structural studies reveal that the molecular structure consists of a β‐Mo₈O₂₆ polyanion with eight MoO₆ distorted edge‐shared octahedra with short terminal Mo–O bonds (1.692–1.714 Å), bonds of intermediate length (1.887–1.999 Å) and long bonds (2.150–2.473 Å). Two different types of hydrogen bonds have been found: N–H···O (2.800–3.075 Å) and C–H···O (3.095–3.316 Å). The presence of π–π stacking interactions and strong hydrogen bonds are presumably responsible for the special disposition of the pyridinic rings around the polyanion cluster.     

The intricacies of the stacking interaction in a pyrrole–pyrrole system

Extensive calculations of potential energy surfaces for parallel-displaced configurations of pyrrole–pyrrole systems have been carried out by the use of a dispersion-corrected density functional. System geometries associated with the energy minima have been found. The minimum interaction energy has been calculated as ?5.38 kcal/mol. However, bonding boundaries appeared to be relatively broad, and stacking interactions can be binding even for ring centroid distances larger than 6 Å. Though the contribution of the correlation energy to intermolecular interaction in pyrrole dimers appeared to be relatively small (around 1.6 smaller than it is in a benzene–benzene system), this system’s minimum interaction energy is lower than those calculated for benzene–benzene, benzene–pyridine and even pyridine–pyridine configurations. The calculation of the charges and energy decomposition analysis revealed that the specific charge distribution in a pyrrole molecule and its relatively high polarization are the significant source of the intermolecular interaction in pyrrole dimer systems.     

Amide–π interactions between formamide and benzene

High‐level ab initio calculations have been carried out using a formamide–benzene model system to evaluate amide–π interactions. The interaction energies were estimated as a sum of the CCSD(T) correlation contribution and the HF energy at the complete basis set limit, for the geometries of the model structures at the energy minimum obtained by potential energy surface (PES) scans. NH/π geometry in a face‐on configuration was found to be the most attractive among the various geometries considered, with interaction energy of ?3.75 kcal/mol. An interaction energy of ?2.08 kcal/mol was calculated for the stacked N/Center type geometry, where the nitrogen atom of formamide points directly toward the center of the aromatic ring. The weakest C?O/π geometry, where a carbonyl oxygen atom points toward the plane of the aromatic ring, was found to have energy minimum at an intermolecular distance of 3.67 Å from the PES, with a repulsive interaction energy less than 1 kcal/mol. However, if there are simultaneous attractive interactions with other parts of the molecule besides the amide group, the weak repulsion could be easily overcome, to give a C?O/π geometry interaction. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2009     

Pentafluorobenzoato‐dimolybdenum(II) Solvate and Co‐crystal Complexes with Benzene and Naphthalin

The quadruply bonded Mo₂⁴⁺ complex Mo₂(DAniF)₃(OOCC₆F₅) ( 1 ) [DAniF = N,N′‐bis(4‐methoxyphenyl)formamidinate] was synthesized. The solvate Mo₂(DAniF)₃(OOCC₆F₅) · (C₆H₆) ( 2 ) and co‐crystal Mo₂(DAniF)₃(OOCC₆F₅) · (C₁₀H₈) ( 3 ) complexes were obtained by self‐assembly of crystals of 1 with benzene and naphthalin, respectively. Compounds 1 , 2 , and 3 were structurally characterized by single‐crystal X‐ray diffraction. In monomer 1 , the Mo–Mo bond length of 2.0874(6) Å is typical for dimolybdenum quadruple bonds. The solvate complex 2 was stabilized by weak π–π stacking interactions between the benzene molecule and the pentafluorophenyl ring (as indicated by a center‐to‐center distance of 3.838(10) Å and a center‐to‐plane distance of 3.712(4) Å between phenyl and pentafluorophenyl ring) and intermolecular C–H ··· F–C interactions (the shortest F ··· H distance is 2.560(2) Å). In complex 3 , a one‐dimensional chain was formed by C–H ··· F–C interactions between the hydrogen atoms in naphthalin and the fluorine atoms in the monomer (H ··· F distances of 2.582(2) Å). Information on the structures in solution of the three crystals was obtained by ¹H NMR spectroscopy.     

Theoretical Study on the Complexes of Benzene with Isoelectronic Nitrogen‐Containing Heterocycles

The π–π interactions between benzene and the aromatic nitrogen heterocycles pyridine, pyrimidine, 1,3,5‐triazine, 1,2,3‐triazine, 1,2,4,5‐tetrazine, and 1,2,3,4,5‐pentazine are systematically investigated. The T‐shaped structures of all complexes studied exhibit a contraction of the C? H bond accompanied by a rather large blue shift (40–52 cm^?1) of its stretching frequency, and they are almost isoenergetic with the corresponding displaced‐parallel structures at reliable levels of theory. With increasing number of nitrogen atoms in the heterocycle, the geometries, frequencies, energies, percentage of s character at C, and the electron density in the C? H σ antibonding orbital of the complexes all increase or decrease systematically. Decomposition analysis of the total binding energy showed that for all the complexes, the dispersion energy is the dominant attractive contribution, and a rather large attraction originating from electrostatic contribution is compensated by its exchange counterpart.     

Monomolecular sheets of propeller‐shaped triethyl 4,4′,4′′‐[benzene‐1,3,5‐triyltris(ethyne‐2,1‐diyl)]tribenzoate deuterochloroform monosolvate

The title compound, C₃₉H₃₀O₆·CDCl₃, has a chemical threefold axis and an approximately planar structure, with an ethoxycarbonyl substituent on each of the terminal benzenes oriented in the same direction, thus forming a propeller‐shaped molecule. This molecule is of particular interest in the field of metal–organic frameworks (MOFs), where its hydrolyzed analogue forms MOF structures with high surface areas. The benzene ring which occupies the centre of the molecule forms π–π interactions to the equivalent benzene ring at a perpendicular distance of 3.32 (1) Å. Centrosymmetric dimers formed in this way are interconnected by intermolecular C—H...π interactions with a rather short H...CgA distance of 2.51 Å (CgA is the centroid of the central benzene ring). The molecules are arranged in regular parallel sheets. Within a sheet, molecules are interconnected via C—H...O interactions where all carbonyl O atoms participate in weak hydrogen bonds as hydrogen‐bond acceptors. Neighbouring sheets are connected through the above‐mentioned π–π and C—H...π interactions.     

Supramolecular interactions in the 2,6‐bis(benzimidazol‐2‐yl)pyridine–terephthalic acid–water (2/1/4) cocrystal

In the title compound, 2C₁₉H₁₃N₅·C₈H₆O₄·4H₂O, the terephthalic acid molecule lies on a crystallographic inversion centre and the H atoms of one water molecule exhibit disorder. The maximum deviation of any atom from the mean plane through the C and N atoms of the 2,6‐bis(benzimidazol‐2‐yl)pyridine molecule is only 0.161 (4) Å. In the crystal structure, the water molecules play an important role in linking the other molecules via hydrogen bonding. The structure forms a three‐dimensional framework via strong intermolecular hydrogen bonding. In addition, there are π–π stacking interactions between the imidazole, pyridine and benzene rings.     

Pyridine–pyridine π–π stacking interactions in penta­carbonyl­[pyridine‐4(1H)‐thione]­tungsten(0)

In the title compound, [W(C₅H₅NS)(CO)₅], the pyridine‐4‐thiol ligand coordinates through the sulfur in the thione mode. The coordination sphere around the W atom is distorted from octahedral geometry by intermolecular hydrogen bonding and steric interactions between the pyridine ring and two CO ligands. An intermolecular pyridine–pyridine ring distance of 3.47 (1) Å indicates π–π stacking interactions between these ligand units.     

BLEEP—potential of mean force describing protein–ligand interactions: I. Generating potential

We have developed BLEEP (biomolecular ligand energy evaluation protocol), an atomic level potential of mean force (PMF) describing protein–ligand interactions. The pair potentials for BLEEP have been derived from high-resolution X-ray structures of protein–ligand complexes in the Brookhaven Protein Data Bank (PDB), with a careful treatment of homology. The use of a broad variety of protein–ligand structures in the derivation phase gives BLEEP more general applicability than previous potentials, which have been based on limited classes of complexes, and thus represents a significant step forward. We calculate the distance distributions in protein–ligand interactions for all 820 possible pairs that can be chosen from our set of 40 different atom types, including polar hydrogen. We then use a reverse Boltzmann methodology to convert these into energy-like pair potential functions. Two versions of BLEEP are calculated, one including and one excluding interactions between protein and water. The pair potentials are found to have the expected forms; polar and hydrogen bonding interactions show minima at short range, around 3.0 Å, whereas a typical hydrophobic interaction is repulsive at this distance, with values above 4.0 Å being preferred. ©1999 John Wiley & Sons, Inc. J Comput Chem 20: 1165–1176, 1999     

Force field studies of cholesterol and cholesteryl acetate crystals and cholesterol–cholesterol intermolecular interactions

To model the physical properties of sterols and related species, an all-atom Class II force field has been derived based on the recently reported CFF93 force field for hydrocarbons. It has been tested using both energy minimization and molecular dynamics (MD) simulations of the low-temperature neutron-diffraction structure of cholesteryl acetate crystals and the X-ray diffraction crystal structure of cholesterol. Thus these studies test the techniques and limitations of high-accuracy crystal simulations as well. Employing energy minimization, all cell vectors and volumes were reproduced to within 2.4% of experimental values. For cholesteryl acetate, the root mean square (rms) deviations between the calculated and experimental bond lengths, angles, and torsions of nonhydrogen atoms are 0.013 Å, 1.2°, and 2.4°, respectively. The corresponding maximum deviations are also very small: 0.027 Å for bond length, 3.2° for angle, and 7.6° for torsion. For cholesterol, good agreement between the calculated and experimental structures was found only when the comparison was limited to atoms with relatively small thermal factors (B_eq < 15 Ų). It was found that for both systems, the MD averaged structures were in better agreement with the experimental ones than the energy minimized structures, since the rms deviations in atom positions are smaller for the MD-averaged structures (0.064 Å for cholesteryl acetate and 0.152 Å for cholesterol) than those for the minimized structures (0.178 Å for cholesteryl acetate and 0.189 Å for cholesterol). The force field was then applied to isolated molecules focusing on the rigidity of the cholesteryl ring and cholesterol–cholesterol interaction energies. It is concluded that the cholesteryl ring is fairly rigid since no major conformational change was observed during an MD simulation of a single cholesterol molecule in vacuo at 500 K, in agreement with condensed phase experiments. Calculations of cholesterol–cholesterol pairs suggest that there are only four low-energy configurations and that it is more useful to describe each molecule as having a plane (flat face) and two grooves rather than as having two (one flat and one rough) faces. This provides some insight into the equilibrium crystal structures. Limited results from a modified Class I (CVFF) force field are presented for comparison. © 1995 by John Wiley & Sons, Inc.     

5‐n‐Butylpyridine‐2‐carboxylate–copper(II) and –iron(III) complexes

In trans‐bis(5‐n‐butyl­pyridine‐2‐carboxyl­ato‐κ²N,O)­bis­(methanol‐κO)copper(II), [Cu(C₁₀H₁₂NO₂)₂(CH₄O)₂], the Cu atom lies on a centre of symmetry and has a distorted octahedral coordination. The Cu—O(methanol) bond length in the axial direction is 2.596 (3) Å, which is much longer than the Cu—­O(carboxylate) and Cu—N distances in the equatorial plane [1.952 (2) and 1.977 (2) Å, respectively]. In mer‐tris(5‐n‐bu­tyl­pyridine‐2‐carboxyl­ato‐κ²N,O)­iron(III), [Fe(C₁₀H₁₂NO₂)₃], the Fe atom also has a distorted octahedral geometry, with Fe—O and Fe—N bond‐length ranges of 1.949 (4)–1.970 (4) and 2.116 (5)–2.161 (5) Å, respectively. Both crystals are stabilized by stacking interactions of the 5‐n‐butyl­pyridine‐2‐carboxyl­ate ligand, although hydrogen bonds also contribute to the stabilization of the copper(II) complex.     

HfNixP – Intercalation of Ni into the Three-Dimensional Compound HfP

The new compound HfNi_xP (x = 0.426(1), crystal structure: P6₃/mmc, a = 3.737(1) Å, c = 12.666(2) Å, V = 153.21(7) ų) has been prepared by arc-melting of HfP with nickel and subsequent annealing at 1400°C. Its crystal structure can be considered as a filled HfP structure, with the Ni atoms inserted into the trigonal prismatic voids of the Hf sublattice. Since the neighboring trigonal Hf₆ prisms are centered by P atoms, each of the three rectangular faces of the Hf₆Ni prism is capped with one P atom. Altogether, the structure of HfNi_xP consists of alternating layers of Hf atoms with the packing sequence AABB . One P and the Ni position are situated between the eclipsed Hf layers, whereas the other P site between the A and B layers is surrounded by six Hf atoms in a staggered arrangement. The calculated density of states (Extended Hückel approximation) points to metallic conductivity; threedimensional metallic behavior is assumed because of the Hf–Hf bonding interactions along all three directions.     

Clathrate solvates of tetra­kis(4‐methoxy­carbonyl­phenyl)porphyrin and its zinc(II)–pyridine complex,in which the porphyrin host structures are stabilized by porphyrin–porphyrin stacking and C—H⋯O attractions

Tetra­kis(4‐methoxy­carbonyl­phenyl)porphyrin, or tetra­methyl 4,4′,4′′,4′′′‐porphyrin‐5,10,15,20‐tetra­benzoate, crystallizes as a nitro­benzene 1.9‐solvate, C₅₂H₃₈N₄O₈·1.9C₆H₅NO₂, (I). The solvent mol­ecules are contained in extended channels which propagate through the host lattice between parallel screw/glide‐related columns of offset‐stacked porphyrin entities. Side packing of these columns involves π–π inter­actions between the methoxy­carbonyl­phenyl residues. Mol­ecules of the porphyrin host lie on crystallographic inversion centres. The zinc(II)–pyridine derivative pyridine­(tetra­methyl 4,4′,4′′,4′′′‐porphyrin‐5,10,15,20‐tetra­benzoato)zinc(II), [Zn(C₅₂H₃₆N₄O₈)(C₅H₅N)], (II), is a square‐pyramidal five‐coordinate complex with pyridine as an apical ligand, which crystallizes as a chloro­form–pyridine solvate. The metallo­porphyrin–pyridine units form an open layered arrangement, occluding the non‐coordinated solvent moieties within the intra­layer inter­porphyrin voids. Within such arrays, the host porphyrin mol­ecules are in contact with one another through the peripheral methoxy­carbonyl substituents. The crystal packing consists of a bilayered arrangement of inversion‐related porphyrin layers, with the axial ligands mutually penetrating into the voids of neighbouring arrays and tight offset stacking of these bilayers.     

Amide hydrogen bonding: control of the molecular and extended structures of two symmetrical pyridine‐2‐carboxamide derivatives

The crystal structures of two symmetrical pyridine‐2‐carboxamides, namely N,N′‐(propane‐1,3‐diyl)bis(pyridine‐2‐carboxamide), C₁₅H₁₆N₄O₂, (I), and N,N′‐(butane‐1,4‐diyl)bis(pyridine‐2‐carboxamide), C₁₆H₁₈N₄O₂, (II), exhibit extended hydrogen‐bonded sequences involving their amide groups. In (I), conventional bifurcated amide–carbonyl (N—H)...O hydrogen bonding favours the formation of one‐dimensional chains, the axes of which run parallel to [001]. Unconventional bifurcated pyridine–carbonyl C—H...O hydrogen bonding links adjacent one‐dimensional chains to form a `porous' three‐dimensional lattice with interconnected, yet unfilled, voids of 60.6 (2) ų which combine into channels that run parallel to, and include, [001]. 4% of the unit‐cell volume of (I) is vacant. Compound (II) adopts a Z‐shaped conformation with inversion symmetry, and exhibits an extended structure comprising one‐dimensional hydrogen‐bonded chains along [100] in which individual molecules are linked by complementary pairs of amide N—H...O hydrogen bonds. These hydrogen‐bonded chains interlock viaπ–π interactions between pyridine rings of neighbouring molecules to form sheets parallel with (010); each sheet is one Z‐shaped molecule thick and separated from the next sheet by the b‐axis dimension [7.2734 (4) Å].     

Pentastrontium Tris[tetraoxovanadate(V)] catena‐Monoxocuprate(I), Sr5(VO4)3(CuO) – An Apatite Derivative with Inserted Linear 1Ë[CuO]1– Chains

Sr₅(VO₄)₃(CuO) was prepared via solid state reactions from mixed powders of the metal oxides or carbonates in corundum crucibles in air (1173–1740 K). The compound is transparent and stable in air. The color changes with the preparation temperature from light gray (1173 K) to gray (1740 K). The crystal structure (space group P6₃/m, No. 176; Z = 2; a = 10.126 Å, c = 7.415 Å) is a derivative of the apatite Ca₅(PO₄)₃OH, and is characterized by isolated [VO₄]^3– anions (d(V–O) = 1.710 Å) and infinite linear ^1∞[CuO]^1– chains (d(Cu–O) = 1.854 Å) inserted in the channels parallel to the hexagonal axis. The compound prepared at 1740 K contains vacancies at the copper and oxygen positions of the linear chains (about 10% and 5%, respectively).     

Molecular “Multi‐rod Cable” {[Co(NC5H4–CH=CH–C6H4–CH=CH–C5H4N)(HCOO)2]8}n: A Novel Supramolecular Architecture by Cooperation of Coordination and Stacking Interactions

The cobalt‐formate coordination polymers {[Co(bpyph)(HCOO)₂]₈}_n ( 1 ) (bpyph = 1,4‐bis(2‐(4‐pyridyl)ethenyl)benzene) and {[Co(HCONH₂)₂(HCOO)₂]}_n ( 2 ) have been prepared by interaction of Co(NO₃)₂ · 6 H₂O in formamide solution with generation of formate anion by hydrolysis of the solvent. Coordination polymer 1 reveals an unprecedented example of “molecular multi‐rod cable” architecture, in which eight single “molecular wires” {[Co(bpyph)]}_n are interlinked by bridging formate anions to give infinite octameric chains. The formate groups adopt mono‐, and bi‐ and tridentate bridging and chelate modes of coordination (Co–O 1.966–2.134 Å). The coordination geometry around the cobalt atoms is essentially dominated by the demands for most effective packing of parallel situated polycyclic aromatic ligands, with extensive CH…π, or edge‐to‐face stacking interactions within the single octameric chain as well as between the closest neighbours (C…C separations within this stack are ca. 3.50 Å).     

Pyridine and 3‐methylpyridine solvates of the triple sulfa drug constitutent sulfamethazine

Sulfonamides display a wide variety of pharmacological activities. Sulfamethazine [abbreviated as SMZ; systematic name 4‐amino‐N‐(4,6‐dimethylpyrimidin‐2‐yl)benzenesulfonamide], one of the constitutents of the triple sulfa drugs, has wide clinical use. Pharmaceutical solvates are crystalline solids of active pharmaceutical ingredients (APIs) incorporating one or more solvent molecules in the crystal lattice, and these have received special attention, as the solvent molecule can impart characteristic physicochemical properties to APIs and solvates, therefore playing a significant role in drug development. The ability of SMZ to form solvates has been investigated. Both pyridine and 3‐methylpyridine form solvates with SMZ in 1:1 molar ratios. The pyridine monosolvate, C₁₂H₁₄N₄O₂S·C₅H₅N, crystallizes in the orthorhombic space group Pna 2₁, with Z = 8 and two molecules per assymetric unit, whereas the 3‐methylpyridine monosolvate, C₁₂H₁₄N₄O₂S·C₆H₇N, crystallizes in the orthorhombic space group P 2₁2₁2₁, with Z = 4. Crystal structure analysis reveals intramolecular N—H…N hydrogen bonds between the molecules of SMZ and the pyridine solvent molecules. The solvent molecules in both structures play an active part in strong intermolecular interactions, thereby contributing significantly to the stability of both structures. Three‐dimensional hydrogen‐bonding networks exist in both structures involving at least one sulfonyl O atom and the amine N atom. In the pyridine solvate, there is a short π–π interaction [centroid–centroid distance = 3.926 (3) Å] involving the centroids of the pyridine rings of two solvent molecules and a weak intermolecular C—H…π interaction also contributes to the stability of the crystal packing.     

Assessing the attractive/repulsive force balance in axial cyclohexane C–Hax···Yax contacts: A combined computational analysis in monosubstituted cyclohexanes

The interactions of axial substituents in monosubstituted cyclohexane rings are studied in this work using an array of different computational techniques. Additionally, the anomalous axial preference for some bulky substituents is related to stabilizing dispersion interactions. We find that the C–H_ax···Y_ax contacts for various substituents with distances ranging from 2 to ～5 Å may include attractive dispersion forces that can affect the conformational equilibrium; these forces co‐exist with Pauli repulsive forces effected by Y_ax group due to van der Waals sphere penetration. At distances between 2 and 3 Å stabilizing electron transfer interactions were calculated and the combination of natural bond orbital and QTAIM analysis showed that, in certain cases, Y_ax = ^tBu, C_ax–O or C_ax = O or S_ax = O or C_ax = S this interaction can be characterized as an improper H‐bond. DFT‐D3 and non‐covalent interactions calculations (NCIs) in cyclohexane derivatives with Y_ax = SiOR₃ including H_Yax···H_cy surfaces at distances ranging between 4 and 6 Å suggest that dispersion has a clear effect on the experimentally observed stabilization of the axial conformer. NCIs computed from the reduced density gradient help to visually identify and analyze these interactions. © 2016 Wiley Periodicals, Inc.