Nature and strength of C-H···O interactions involving formyl hydrogen atoms: computational and experimental studies of small aldehydes

Structural and electronic properties of C-H···O contacts in compounds containing a formyl group are investigated from the perspective of both hydrogen bonding and dipole-dipole interactions, in a systematic and graded approach. The effects of α-substitution and self-association on the nature of the formyl H-atom are studied with the NBO and AIM methodologies. The relative dipole-dipole contributions in formyl C-H···O interactions are obtained for aldehyde dimers. The stabilities and energies of aldehyde clusters (dimer through octamer) have been examined computationally. Such studies have an implication in crystallization mechanisms. Experimental X-ray crystal structures of formaldehyde, acrolein and N-methylformamide have been determined in order to ascertain the role of C-H···O interactions in the crystal packing of formyl compounds.     

First systematic investigation of C-H...Cl hydrogen bonding using inorganic supramolecular synthons: lamellar, stitched stair-case, linked-ladder, and helical structures

Using a group of six neutral M(II)Cl(2)-containing coordination compounds as building blocks, the first systematic investigation of C-H...Cl hydrogen-bonding interactions was performed. Single-crystal X-ray structural analyses of four new compounds (pseudo-tetrahedral Co(II) and Zn(II); distorted trigonal bipyramidal Zn(II)) authenticate the metal coordination geometry. To provide a unified view of the presence of noncovalent interactions in this class of compounds, we have re-examined the packing diagram of two previously reported compounds (a distorted square-pyramidal Cu(II) complex and a trans-octahedral Co(II) complex). The organic ligands of our choice comprise bidentate/tridentate pyrazolylmethylpyridines and an unsymmetrical tridentate pyridylalkylamine. This systematic investigation has allowed us to demonstrate the existence of versatile C-H...Cl(2)M interactions and to report the successful application of such units as inorganic supramolecular synthons. Additional noncovalent interactions such as C-H...O and O-H...Cl hydrogen bonding and pi-pi stacking interactions have also been identified. Formation of novel supramolecular architectures has been revealed: 2D lamellar (p-cyclophane) and 3D lamellar, 3D "stitched staircase" (due to additional hydrogen-bonding interactions by water tetramers, with an average O-O bond length in the tetramer unit of 2.926 A, acting as "molecular clips" between staircases), 3D linked ladder, and single-stranded 1D helix.     

Crystal and molecular structures of (3Z)-(±)-4-(2′-hydroxypropyl)amino-and (3Z)-4-(2′-hydroxyethyl)amino-pent-3-en-2-ones

An X-ray study of (3Z)-(±)-4-(2′-hydroxypropyl)amino-and (3Z)-4-(2′-hydroxyethyl)amino-pent-3-en-2-ones is reported. The bond lengths inside the H ring are equalized due to the classical N-H...O hydrogen bond between the carbonyl oxygen and the amino group. In the 4-(2′-hydroxyethyl)amino-pent-3-en-2-one crystal, due to the classical N-H...O bonds, infinite zigzag chains are formed along the 0b axis and arranged into a layered structure due to the weak C-H...O interactions. In (±)-4-(2′-hydroxypropyl)aminopent-3-en-2-one crystal, however, centrosymmetric dimers are formed, which are then linked by weak C-H...O intermolecular interactions to form a layered structure along the a0b plane.     

Synthesis and structure of a sodium complex of an aromatic beta-diketone and pyrazolylpyridine

Reaction of NaH with a THF solution of Eu(BTA)3(pypzH) [BTA = 1-benzoyl-3,3,3-trifluoroacetonate, pypzH = 2-(3-pyrazolyl)pyridine] leads to the formation of the europium-free tetrasodium complex [Na(4)(pypzH)(2)(micro4-BTA)(2)(micro2-BTA)(2)]. Single-crystal X-ray diffraction studies revealed the presence of a centrosymmetric Na+ hybrid tetramer,which fully occupies the contents of the triclinic unit cell. The crystal structure contains two individual Na+ cations, Na(1) and Na(2), which have highly irregular [NaN(2)O(3)] and[NaO(6)] local coordination environments, respectively. One of the key features is the presence of a central [Na(4)O(6)] core, which is unprecedented for Na+ . Externally to this [Na(4)O(6)] cluster pyrazolylpyridine organic molecules are N,N-chelated to Na(1). Even though all of the organic residues contain aromatic rings, the crystal packing of individual centrosymmetric tetrasodium [Na(4)(pypzH)(2)(micro4-BTA)(2)(micro2-BTA)(2)] molecular moieties is essentially driven through geometrical aspects combined with weak C-H...pi interactions, rather than the expected a priori pi-pi interactions. The material also contains classical strong hydrogen bonds, even though these do not directly contribute to the packing driving forces.     

Self-sorting molecular clips

We report the synthesis and characterization of 12 C-shaped methylene-bridged glycoluril dimers (1-12) bearing H-bonding groups on their aromatic rings. Compounds 1, 2, (+/-)-4a, (+/-)-5, (+/-)-7, and 8 form tightly associated homodimers in CDCl3, due to the combined driving force of pi-pi and H-bonding interactions. Compounds 2, (+/-)-5, and 8, having disparate spatial distribution of their H-bonding groups, display the ability to efficiently distinguish between self and nonself even within three-component mixtures in CDCl3. When the spatial distributions of the H-bonding groups of the molecular clips are similar (e.g., 1 and 2), a mixture of homodimers and heterodimers is formed. The effect of various structural modifications (e.g., chirality, side chain steric bulk, number and pattern of H-bonds) on the strength of self-assembly and the fidelity of self-sorting are presented. On the basis of these results we prepared self-sorting systems comprising three (e.g., 1, (+/-)-5, and (+/-)-7) and even four ( 2, (+/-)-5, 9, and 10) components. The potential of molecular clips 1-12 as robust, functionalizable, self-sorting modules to control the noncovalent interaction network in systems chemistry studies is described.     

Molecular catenation via metal-directed self-assembly and pi-donor/pi-acceptor interactions: efficient one-pot synthesis, characterization, and crystal structures of [3]catenanes based on Pd or Pt dinuclear metallocycles

Dinuclear square metallocycles 3a,b assemble spontaneously when M(en)(OTf)2 (M = Pd, Pt) and a 4,4'-bipyridinium ligand are mixed in acetonitrile. Six new [3]catenanes were prepared in good yields by thermodynamically driven self-assembly reaction of molecular squares 3a,b and pi-complementary dioxoaryl cyclophanes. Single-crystal X-ray analyses of the [3]catenanes revealed the insertion of two aromatic units inside the metallocycle cavity. The structures are stabilized by means of a combination of pi-pi stacking, [C-H...pi] interactions, and [C-H...O] hydrogen bonds. [3]Catenane (DB24C8)2-(3a) showed in solid-state two external DB24C8 rings positioned over the Pd(en) corners, which are held in position by [N-H...O] hydrogen bonds. Furthermore, formation of catenane (DB24C8)2-(3a) can be switched off and on in a controllable manner by successive addition of KPF6 and 18-crown-6.     

Heterodimetallic germanium(IV) complex structures with transition metals

The hydrothermal synthesis and structural characterization of a number of complex compounds containing the divalent tris(oxalato-O,O')germanate anion, [Ge(C2O4)3]2-, or the neutral bis(oxalate-O,O')germanium fragment, [Ge(C2O4)2], with transition-metal (M) cationic complexes of 1,10'-phenanthroline (phen) is reported: [M(phen)3][Ge(C2O4)3].xH2O [where M2+ = Cu2+ (1a and 1b), Fe2+ (2a and 2b), Ni2+ (3), Co2+ (4); x = 0.2 for 2b], [MGe(phen)2(mu2-OH)2(C2O4)2] [where M2+ = Cd2+ (5) and Cu2+ (6)]. The isolation of two polymorphs with Cu2+ (1a and 1b) and other pseudo-polymorphs for Fe2+ (2a and 2b) was rationalized based on slightly different molar ratios for the starting materials. All compounds have been characterized using EDS, SEM, vibrational spectroscopy (FT-IR and FT-Raman), thermogravimetry, and CHN elemental composition and their structure determined on the basis of single-crystal X-ray diffraction studies. The crystal packing of the different chemical moieties for each series of compounds was discussed on the basis of the various intermolecular interactions present (strong C-H...pi and weak C-H...O hydrogen-bonding interactions, C-H...pi and pi-pi contacts).     

α-Indolyl-β-nitroacrylates. Synthesis and structure

A one-pot procedure has been developed for the synthesis of α-indolyl-β-nitroacrylates by reaction of β-bromo-β-nitroacrilates with indole and substituted indoles. All indolylnitroacrilates thus obtained have Z configuration of the double bond. According to the X-ray diffraction data, ethyl 2-(1-methyl-1H-indol-3-yl)-3-nitroacrylate is characterized by s-trans conformation of the double C=C bond and indole ring; its crystal packing involves intermolecular hydrogen bonds C-H…O and C-H…π with formation of centrosymmetric dimers which give rise to bilayer supramolecular structures.     

Self-association and self-assembly of molecular clips in solution and in the solid state

Clip molecules based on diphenylglycoluril form well-defined dimeric structures in chloroform solution and in the solid state. In solution the dimerization process is based on favourable π-π interactions and cavity filling effects. A combination of favourable π-π interactions and crystal packing forces determine the self-assembly of clips in the solid state. The geometry that the clip molecules adopt in solution and in a series of X-ray crystal structures is compared with favourable geometries predicted by molecular modelling calculations.     

Molecular Pair Analysis: C?H⋅⋅⋅F Interactions in the Crystal Structure of Fluorobenzene? And Related Matters

The crystal structure of fluorobenzene is compared with isomorphous crystal structures of molecules of roughly similar shape. The lowest-energy fluorobenzene dimers are identified by theoretical calculations. Molecular pair analysis of the crystal structure of fluorobenzene and of an isomorphous virtual low-energy polymorph of benzene suggests that the important intermolecular interactions in the two structures are closely similar. In particular, the intermolecular C-H...F interactions in the fluorobenzene crystal have approximately the same structure-directing ability and influence on the intermolecular energy as the corresponding C-H...H interactions in benzene. Molecular pair analysis of the isomorphous crystal structures of benzonitrile, alloxan, and cyclopentene-1,2,3-trione indicates that essentially the same crystal structure can be adopted with quite different patterns of pair energies and atom-atom interactions. The question as to whether the packing radius of organic fluorine is larger or smaller than that of hydrogen, is addressed, but not answered.     

Understanding the structural properties of a homologous series of bis-diphenylphosphine oxides

A homologous series of bis-diphenylphosphine oxides (C6H5)2PO(CH2)(n)PO(C6H5)2 (with n = 2-8; denoted 2-8] have been investigated to explore the effects of a range of competing and cooperative intermolecular and intramolecular interactions on the structural properties in the solid state. The important factors influencing the structural properties include intramolecular aspects such as the conformation of the aliphatic chain and the intramolecular interaction between the two P=O dipoles in the molecule, and intermolecular aspects such as long-range electrostatic interactions (dominated by the arrangement of the P=O dipoles), C-H...O interactions, C-H...pi interactions and pi...pi interactions. Compounds 3 and 5 could be crystallized only as solvate co-crystals (3 water and 5 x (toluene)2], whereas the crystal structures of all the other compounds contain only the bis-diphenylphosphine oxide molecule. The crystal structures have been determined from single-crystal X-ray diffraction data, with the exception of 7 (which has been determined here from powder X-ray diffraction data) and 4 (which was known previously). The compounds with even n represent a systematic structural series, exhibiting characteristic, essentially linear P=O...P=O...P=O dipolar arrays, together with C-H...O and C-H...pi interactions. For the compounds with odd n, on the other hand, uniform structural behaviour is not observed across the series, although certain aspects of these crystal structures contribute in a general sense to our understanding of the structural properties of bis-diphenylphosphine oxides. Importantly, for the compounds with odd n, there is "frustration" with regard to the molecular conformation, as the preferred all-anti conformation of the aliphatic chain gives rise to an unfavourable parallel alignment of the two P=O dipoles within the molecule. Clearly the importance of avoiding a parallel alignment of the P=O dipoles becomes greater as n decreases. Local structural aspects (investigated by high-resolution solid-state 31P NMR spectroscopy) and thermal properties of the bis-diphenylphosphine oxide materials are also reported.     

Helical self-assembly of substituted benzoic acids: influence of weaker X...X and C-H...X interactions

The X-ray crystal packing analyses of the sterically encumbered halogen-substituted benzene carboxylic acids 1-4 reveal a novel and unprecedented crystal packing in that the association of the carboxyl groups through O-H...O bonds results in the generation of a helix along the 41-screw axis. Such an organization of the acids is shown convincingly to be a result of the close packing, which exploits the weaker X...X and C-H...X interactions in conjunction with the stronger O-H...O hydrogen bonds. In contrast, the chloro- and bromo-substituted durene carboxylic acids 6 and 7 exhibit a pattern that is akin to tape/ribbon involving the centrosymmetric-dimer motif and X...X short intermolecular interactions. The structural investigations demonstrate the ability of the weaker interactions in modifying the supposedly "robust" centrosymmetric-dimer motif of the carboxyl groups in a decisive manner.     

Polymeric silver(I) complexes with pyridyl dithioether ligands: experimental and theoretical investigations on the coordination properties of the ligands

The reactions of four flexible tetradentate ligands, 1,3-bis(2-pyridylthio)propane (L1), 1,4-bis(2-pyridylthio)butane (L2), 1,5-bis(2-pyridylthio)pentane (L3) and 1,6-bis(2-pyridylthio)hexane (L4) with AgX (X = BF4-, ClO4-, PF6-, or CF3SO3-) lead to the formation of seven new complexes: [AgL1(BF4)]2 (1), [[AgL2](ClO4)]infinity (2), [[AgL2(CH3CN)](PF6)]infinity (3), [[AgL3](BF4)(CHCl3)]2 (4), [[AgL3(CF3SO3)](CH3OH)(0.5)]infinity (5), [[Ag2L4(2)](BF4)2]infinity (6), and [[AgL4](PF6)]infinity (7), which have been characterized by elemental analyses, IR spectroscopy, and X-ray crystallography. Single-crystal X-ray analyses show that complexes 1 and 4 possess dinuclear macrometallacyclic structures, and complexes 2, 3 and 5-7 take chain structures. In all the complexes, the nitrogen atoms of ligands preferentially coordinate to silver atoms to form normal coordination bonds, while the sulfur atoms only show weak interactions with silver atoms and the intermolecular AgS weak contacts connect the low-dimensional complexes into high-dimensional supramolecular networks. Additional weak interactions, such as pi-pi stacking, F...F weak interactions, Ag...O contacts or C-H...O hydrogen bonds, also help to stabilize the crystal structures. It was found that the parity of the -(CH2)n- spacers (n = 3-6) affect the orientation of the two terminal pyridyl rings, thereby significantly influence the framework formations of these complexes. The coordination features of ligands and their conformation changes between free and coordination states have been investigated by DFT calculations.     

Does the most stable formic acid tetramer have pi stacking or C-H...O interactions?

Density functional theory (DFT), Moller-Plesset (MP) perturbation theory, and coupled-cluster calculations are used to examine low-energy minima on the potential energy surface of the formic acid tetramer (HCOOH)(4). The potential energy surface is rather flat with respect to rotation of one of the dimers, relative to the other dimer in an aligned stack, about the axis passing through the inversion centers of the dimers. Our best calculations suggest that an aligned pi-pi stack of two dimers is very likely to be the global minimum but there are two other pi-pi stacks within 0.5 kcal /mol. Moreover, a fourth pi-pi stack, a planar association of two dimers held together by C-H...O interactions, and a bowl structure all lie within 1 kcal /mol of the lowest-energy structure.     

Dinuclear triple helicates with diazine ligands: X-ray structural, electrochemical, and magnetic studies

A series of dinuclear complexes of Mn(III), Fe(III), and Co(III) with two diazine Schiff bases, H2salhn and H2mesalhn, is reported. The Schiff bases are prepared by condensation reactions of hydrazine with salicylaldehyde (H2salhn) and with 2-hydroxyacetophenone (H2mesalhn) in 1:2 mol ratio. X-ray crystallographic characterization reveals triple helical structures of [Co2(salhn)3], [Co2(mesalhn)3], and [Fe2(mesalhn)3]. In each complex, three dinucleating O,N,N,O donor ligands provide three diazine (=N-N=) bridges between the metal ions and facial O3N3 coordination spheres around them. The ligands are twisted about the N-N single bond and coordinate to the two metal ions in a helical fashion to generate the triple helical structure. The dicobalt(III) complex of mesalhn2- is D3-symmetric, while the diiron(III) analogue is very close to being of this symmetry. On the other hand, the dicobalt(III) complex of salhn2- significantly deviates from the ideal D3-symmetry due to the large range covered by the twist angles of the three ligands. In the crystal lattice of these complexes, intermolecular C-H...O, C-H...N, O-H...O, C-H...Cl, and pi-pi interactions involving the complex and the solvent molecules lead to one- and two-dimensional supramolecular structures. The complexes [Fe2(mesalhn)3] and [Co2(mesalhn)3] are redox active and display two successive metal-centered reductions on the cathodic side of Ag/AgCl reference electrode. Weak antiferromagnetic spin-coupling is operative between the two metal ions in [Mn2(salhn)3] (J = -0.57(1) cm(-1)) and in [Fe2(mesalhn)3] (J = -2.82(4) cm(-1)).     

Mimicking [2,2]paracyclophane topology: molecular clips for the coordination-driven cofacial assembly of pi-conjugated systems

Self-assembly of CuI dimers, featuring a bridging phosphole ligand, and ditopic cyano-substituted chromophores affords nanosize supramolecular cationic rectangles. Due to the short Cu-Cu distance in the bimetallic clips, the coordinated chromophores are forced to participate in cofacial pi-pi interactions as evidenced by X-ray data. In addition, intermolecular pi-pi interactions in the solid state are observed leading to infinite columns of pi-stacked (para-phenylenevinylene)-based chromophores.     

The unexpected and large enhancement of the dipole moment in the 3,4-bis(dimethylamino)-3-cyclobutene-1,2-dione (DMACB) molecule upon crystallization: a new role of the intermolecular CH...O interactions.

The molecular dipole moment of the 3,4-bis(dimethylamino)-3-cyclobutene-1,2-dione (DMACB) molecule and its enhancement in the crystal was evaluated by periodic RHF ab initio computations. A discrete boundary partitioning of the electronic density that allows an unambiguous partitioning of the molecular space in the condensed phase was adopted. The resulting molecular dipole in the crystal compares favorably with the experimental value obtained by a multipolar analysis of single-crystal X-ray diffraction data recorded at 20 K, using a fuzzy boundary partitioning of the derived pseudoatom densities. We show that a large and highly significant molecular dipole enhancement may occur upon crystallization, despite the lack of a strongly hydrogen bonded environment in the crystal. The 23 unique C-H...O interactions which are formed upon packing of the DMACB molecule induce an increase in the molecular dipole (over 75%) that is comparable to or greater than that found in systems which are characterized by the stronger O-H...O and N-H...O hydrogen bonds. The DMACB molecule constitutes an excellent system for the study of C-H...O interactions in the condensed phase, since no other kind of competing hydrogen bonds is present in its crystal. A simple and qualitative model for the matrix contribution to the DMACB molecular dipole enhancement in the crystal is proposed. The formation of several weak C-H...O bonds is found to yield a small (about 0.2 e) net flux of electronic charge flowing from the hydrogens of the methyl groups to the carbonyl oxygen atoms. Despite the limited increase of the intramolecular charge transfer upon crystallization, a large molecular dipole enhancement occurs because the centroids of the positive and negative induced charges are quite far apart. This work highlights a new and important role of the C-H...O bond, besides those already known in the literature.     

The first observation of nitrogen-carbonyl bonding: self-assembly of N-oxalyl 2,4-dinitroanilide assisted by a weak N...O=C interaction

A new type of weak bond, i.e., the N...O=C interaction, that determines the crystal packing of N-oxalyl 2,4-dinitroanilide (1) in cooperation with C-H...O hydrogen bonds, has been found and is rationalized by ab initio calculations as being the result of electrostatic interactions.     

Silver(I) complexes in coordination supramolecular system with bulky acridine-based ligands: syntheses, crystal structures, and theoretical investigations on C-H...Ag close interaction

In our efforts to investigate the coordination architectures of transition metals and organic ligands with tailored structures, we have prepared two structurally related rigid bulky acridine-based ligands, 9-[3-(2-pyridyl)pyrazol-1-yl]- acridine (L(1)) and 9-(1-imidazolyl)acridine (L2), and synthesized and characterized four of their Ag(I) complexes, {[AgL1](ClO4)}2 (1), {[AgL1](NO3)}2 (2), [AgL2(2)](ClO4) (3), and {[(Ag3L2(3))(NO3)](NO3)2(H2O)}(infinity) (4). The single-crystal X-ray diffraction analysis shows that the structures of 1 and 2 are similar to each other, with the two intramolecular Ag(I) centers of each complex being encircled by two L1 ligands; this forms a unique boxlike cyclic dimer, which is further linked to form one-dimensional (1D) chains of 1 and a two-dimensional (2D) network of 2 by intermolecular face-to-face pi...pi stacking and/or weak C-H...O hydrogen-bonding interactions, respectively. 3 has a mononuclear structure, which is further assembled into a 2D network via intermolecular Ag...O and pi...pi stacking weak interactions. 4 possesses two different 1D motifs that are further interlinked through interlayer face-to-face pi...pi stacking and Ag...O weak interactions, resulting in a 2D network. It is worth noting that one of the interesting structural features of 1, 2, and 4 is the presence of obvious C-H...M hydrogen-bonding interactions between the Ag centers and some acridine ring H atoms identified by X-ray diffraction on the basis of the van der Waals radii. Furthermore, as a representative example, full geometry optimization on the basis of the experimental structure, the natural bond orbital (NBO), and topological analysis of 1 were carried out by DFT and AIM (Atoms in Molecules) calculations. The total C-H...Ag interaction energy in 1 is estimated to be about 14 kJ/mol. Therefore, this work offers three new rare examples (1, 2, and 4) that exhibit C-H...Ag weak interactions, in which the N donors of the acridine rings coordinate to Ag(I) ions. Also, these results strongly support the existence of C-H...Ag close interactions and allow us to have a better understanding of the nature of such interactions in the coordination supramolecular systems.     

Interpretation of the multiple vanadium-oxygen bonds in the central VO(eta2-O2)+ group. Synthesis, structure, supramolecular interactions and DFT studies for complexes with 2,2'-bipyridine, 1,10-phenanthroline, pyrazinato(1-) and pyrazinamide ligands

Neutral peroxovanadium(v) complexes, [VO(O2)(pca)(bpy)] (1), [VO(O2)(pca)(phen)] (2) and [VO(O2)(pic)(pcaa)(H2O)].H2O(3), were synthesized [2,2'-bipyridine (bpy), 1,10-phenanthroline (phen), pyrazinecarboxamide (pcaa), 2-pyrazinecarboxylic (Hpca) and picolinic (Hpic) acids]. Their X-ray single crystal analysis revealed a distorted pentagonal bipyramidal geometry in all complex molecules. The four "free" coordination sites of the vanadium atoms of the VO(eta2-O2)+ moieties in 1 and 2 are occupied by the donor atoms of two bidentate heteroligands. The supramolecular structures of 1 and 2 are exclusively constructed by intermolecular C--H(ar)...O hydrogen bonds [dH(H...O): 2.292-2.708 A (1), and 2.260-2.720 A (2)]. In addition, the structures are stabilized by parallel off-set pi-pi interactions between the bpy rings resp. non-parallel off-set interactions between the phen rings [centroid distances: 3.7000(1) A (1), 3.9781(2) and 3.6757(2) A (2)]. In the molecular structure of 3, pcaa is coordinated in an equatorial position of the bipyramid via the nitrogen atom of the pyrazine ring, while the aqua ligand is in the apical position. The disordered crystal water molecules are located in 1D channels oriented along the a axis. The intermolecular C-H(ar)...O hydrogen bonds in 3 were found within the dH(H..O) range 2.409-2.669 A. The pic ligands are off-set pi-pi stacked, with centroid distances: 3.6725(3) and 3.8323(3) A. The DFT orbital calculations and NBO analysis for the VO(eta2-O2)+ group gave evidence for a triple V[triple bond]O bond, and showed that the observed cis arrangement of the oxo and peroxo ligands results from the direct interaction between them. Experimental and calculated UV-Vis and IR spectral data are presented.