Recurrence of carboxylic acid-pyridine supramolecular synthon in the crystal structures of some pyrazinecarboxylic acids.

X-ray crystal structures of pyrazinic acid 1 and isomeric methylpyrazine carboxylic acids 2-4 are analyzed to examine the occurrence of carboxylic acid-pyridine supramolecular synthon V in these heterocyclic acids. Synthon V, assembled by (carboxyl)O-H...N(pyridine) and (pyridine)C-H...O(carbonyl) hydrogen bonds, controls self-assembly in the crystal structures of pyridine and pyrazine monocarboxylic acids. The recurrence of acid-pyridine heterodimer V compared to the more common acid-acid homodimer I in the crystal structures of pyridine and pyrazine monocarboxylic acids is explained by energy computations in the RHF 6-31G* basis set. Both the O-H.N and the C-H...O hydrogen bonds in synthon V result from activated acidic donor and basic acceptor atoms in 1-4. Pyrazine 2,3- and 2,5-dicarboxylic acids 10 and 11 crystallize as dihydrates with a (carboxyl)O-H...O(water) hydrogen bond in synthon VII, a recurring pattern in the diacid structures. In summary, the carboxylic acid group forms an O-H...N hydrogen bond in pyrazine monocarboxylic acids and an O-H...O hydrogen bond in pyrazine dicarboxylic acids. This structural analysis correlates molecular features with supramolecular synthons in pyridine and pyrazine carboxylic acids for future crystal engineering strategies.     

Co-crystallization of glycine anhydride with the hydroxybenzoic acids: Controlled formation of dimers via synthons cooperation and structural characterization

The results of crystallographic analyses on 1:1 and 1:4 well-defined co-crystals formed between glycine anhydride and each of 4-hydroxybenzoic acid and 3,5-dihydroxybenzoic acid are described. Neutral molecules are connected via heteromeric O-H···O and N-H···O contacts leading to different packing arrangements of supramolecular chains. On the basis of the molecular structures of glycine anhydride and carboxylic acid guests, the hydrogen bonds are arranged to give centrosymmetric synthons V and VII which are noteworthy for their robustness. Hydrogen-bond interactions between glycine anhydride and aromatic acid provide sufficient driving force to direct molecular recognition and crystal packing. Utilization of the orientation of functional groups of the building blocks, the acidity, and weak interactions provides a route for the creation of novel supra- molecular architectures in the crystal lattice. Both two co-crystals contain the expected hydrogen-bonded motifs, and there has been no proton transfer from either of the two carboxylic acids to the aza compound moiety. This demonstrates that glycine anhydride is very capable of affecting the construction of binary co-crystals in a predictable and rationale manner. It is noted that synthons VⅢ and IX are fairly large, but the real challenge in crystal engineering is to find a big enough synthon that occurs often enough. Thermal stability of these compounds has been investigated by thermogravimetric analysis (TGA) of mass loss.     

Three-dimensional supramolecular architecture based on 4,4′-methylene-bis(benzenamine) and aromatic carboxylic acid guests: Synthons cooperation, robust motifs and structural diversity

The two-component solid forms involving 4,4??-methylene-bis(benzenamine) included both salts and co-crystals, while 4,4??-methylene-bis(benzenamine) crystallized exclusively as a salt, in agreement with the differences in the pK _a values. Many of the crystal structures displayed either the neutral or the ionic form of the carboxylic acid-amino heterosynthon, and the similarity in crystal structures between the neutral and the ionized molecules makes the visual distinction between a salt and co-crystal dependent on the experimental location of the acidic proton. A variety of supramolecular hydrogen bonded motifs involving interactions between the aza molecules and carboxylic acid groups are observed rather than just the O-H??N/O-H??O motif. The motifs are identical in all the two compounds analyzed showing the robustness of these supramolecular synthons. In all adducts, recognition between the constituents is established through either N-H??O and/or O-H??O/O-H??N pairwise hydrogen bonds. In all adducts, COOH functional groups available on 1 and 2 interact with the N-donor compounds. The COOH moieties in 1 forms only single N-H??O hydrogen bonds, whereas in 2, it forms pairwise O-H??N/N-H??O hydrogen bonds. The supramolecular architectures are elegant and simple, with stacking of networks in 2, but a rather complex network with a threefold interpenetration pattern was found in 1. Thermal stability of these compounds has been investigated by thermogravimetric analysis (TGA) of mass loss.     

Cocrystallization of N-donor type compounds with 5-sulfosalicylic acid: The effect of hydrogen-bonding supramolecular architectures

Benzotriazole,N,N’-dimethylpiperazine and N-methylpiperazine were applied to crystallize with 5-sulfosalicylic acid(5-H2SSA),affording three new binary molecular cocrystals [(C6H6N3+).(C7H5O6S-)].H2O(1),[(C6H16N22+)1/2.(C7H5O6S-)].H2O(2) and [(C5H14N22+).(C7H5O6S-)2].3H2O(3) under general conditions.Proton-transferring occurs from acid to nitrogen of N-donor compounds in all compounds 1,2 and 3.Analysis of the hydrogen-bonding synthons and their effects on crystal packing were also presented in the context of crystal engineering and host-guest chemistry.In compound 1,1-D infinite chains are extended to a 2-D layered architecture via strong O-H...O hydrogen bonds and then to a 3-D network by N-H...O interactions.Compound 2 and 3 both have the 1-D chain which is formed by O-H...O bonds and weak C-H...O hydrogen bonds.A common intramolecular S(6) [synthon I] ring is formed by the hydroxyl with the carboxyl group in all three compounds.     

Very strong C-H...O, N-H...O, and O-H...O hydrogen bonds involving a cyclic phosphate.

Very short C-H...O, N-H...O, and O-H...O hydrogen bonds have been generated utilizing the cyclic phosphate [CH2(6-t-Bu-4-Me-C6H2O)2]P(O)OH (1). X-ray structures of (i) 1 (unsolvated, two polymorphs), 1...EtOH, and 1...MeOH, (ii) [imidazolium](+)[CH2(6-t-Bu-4-Me-C6H2O)2PO2](-)...MeOH [2], (iii) [HNC5H4-N=N-C5H4NH](2+)[(CH2(6-t-Bu-4-Me-C6H2O)2PO2)2](2-)...4CH3CN...H2O [3], (v) [K, 18-crown-6](+)[(CH2(6-t-Bu-4-Me-C6H2O)2P(O)OH)(CH2(6-t-Bu-4-Me-C6H2O)2PO2)](-)...2THF [4], (vi) 1...cytosine...MeOH [5], (vii) 1...adenine...1/2MeOH [6], and (viii) 1...S-(-)-proline [7] have been determined. The phosphate 1 in both its forms is a hydrogen-bonded dimer with a short O-H...O distance of 2.481(2) [triclinic form] or 2.507(3) A [monoclinic form]. Compound 2 has a helical structure with a very short C-H...O hydrogen bond involving an imidazolyl C-H and methanol in addition to N-H...O hydrogen bonds. A helical motif is also seen in 5. In 3, an extremely short N-H...O hydrogen bond [N...O 2.558(4) A] is observed. Compounds 6 and 7 also exhibit short N-H...O hydrogen bonds. In 1...EtOH, a 12-membered hydrogen-bonded ring motif, with one of the shortest known O-H...O hydrogen bonds [O...O 2.368(4) A], is present. 1...MeOH is a similar dimer with a very short O(-H)...O bond [2.429(3) A]. In 4, the deprotonated phosphate (anion) and the parent acid are held together by a hydrogen bond on one side and a coordinate/covalent bond to potassium on the other; the O-H...O bond is symmetrical and very strong [O...O 2.397(3) A].     

Dimers of formic acid, acetic acid, formamide and pyrrole-2-carboxylic acid: an ab initio study

The intermolecular hydrogen bonds in dimers of formic acid, acetic acid, and formamide were investigated. Additionally, three configurations of the pyrrole-2-carboxylic acid (PCA) dimer were studied to analyze how the pyrrole pi-electron system influences the carboxylic groups connected by double O-H...O hydrogen bonds. The ab initio calculations for the systems investigated were performed at MP2/6-311++G(d,p), MP2/aug-cc-pVDZ, and MP2/aug-cc-pVTZ//MP2/aug-cc-pVDZ levels of theory. The "atoms in molecules" theory of Bader was used and the analysis of the critical points was performed to study the nature of hydrogen bonds. The decomposition of the total interaction energy applied here reveals that the delocalization energy term is a particularly important attractive contribution in these systems, more important in the case of systems forming homonuclear O-H...O double hydrogen bonds than in the case of those connected through heteronuclear N-H...O bonds. Because the systems analyzed may be formally classified as the resonance-assisted hydrogen bonds (RAHBs), it seems that the dominant contribution from the delocalization interaction energy term is a distinguished feature of such interactions.     

Interanionic (-)O-H...O(-) interactions: a solid-state and computational study of the ring and chain motifs

The (-)O-H...O(-) interaction formed by the anions HCO3-, HCO4, HC4O4 and HC5O5- (HA-), obtained upon monodeprotonation of the corresponding carbonic, oxalic, squaric and croconic acids (H2A), has been investigated theoretically and experimentally. The ring (RING) and chain (CHAIN) hydrogen bond motifs established between these anions have been analysed in terms of geometry and energy and their occurrence in crystalline salts investigated by searching the Cambridge Structural Database (CSD) and the Inorganic Chemistry Structural Database (ICSD). It has been shown that hydrogen carbonates form RINGs, with the notable exception of NaHCO3, while only CHAINs are known for hydrogen oxalates. Hydrogen squarates and hydrogen croconates can form both RINGs and CHAINs. The structures of Rb- and Cs- hydrogen croconates, which present the two alternative motifs, have been discussed together with that of the hydrated salt NaHC5O5.H2O. The relationship between RING and CHAIN has been examined in the light of ab initio calculations. A rigorous quantum chemical study of the nature of the interanionic (-)O-H...O(-) interaction in both vacuum and condensed phase has shown that the interaction energy is dominated by the electrostatic component which becomes attractive at short O...O distances (less than 2.5 A) if the net ionic charge on the anion is delocalised away from the -OH group. It has been demonstrated that the RING motif is slightly metastable with respect to dissociation in the gas phase, but becomes stable in the crystal owing to the influence of the Madelung field. However, the CHAIN motif is unstable both in the gas phase and in the crystal. It is argued that interanionic (-)O-H...O(-) interactions ought to be regarded as stabilising bonding interactions rather than proper intermolecular hydrogen bonds because the RING and CHAIN aggregates are not energetically stable on an absolute scale of bonding energy (i.e., in the absence of counterions). The presence of very short non-hydrogen-bridged O...O contacts resulting from charge compression of polyatomic anions bridged by alkali cations is also discussed.     

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.     

Creation of hydrogen bonded 1D networks by co-crystallization of N,N'-bis(2-pyridyl)aryldiamines with dicarboxylic acids

The preparation and crystal structures of fourteen complexes of N,N'-bis(2-pyridyl)aryldiamines with dicarboxylic acids and two complexes with squaric acid are reported. The recognition between the carboxylic acids and the 2-aminopyridine units occurs through the formation of the cyclic R(2)2 (8) hydrogen bond motif, whereas squaric acid creates the analogous R(2)2 (9) motif. In the 1:1 complexes the cyclic motifs generate infinite hydrogen-bonded 1D networks with the alternating component molecules. These networks are further organised into densely packed layers assembled through weaker C-H...O interactions. Analysis of the intermolecular interactions in these complexes led us to the synthesis of N,N'-bis(2-pyridyl)-2,2'-oxybis(aminobenzene) (5) which acts as a tritopic receptor of the carboxylic group and forms exclusively 2:1 complexes with dicarboxylic acids.     

pi-H...O hydrogen bonds: multicenter covalent pi-H interaction acts as the proton-donating system

The MP2 method and the Pople-style basis sets 6-311++G(d,p), 6-311++G(2df,2pd), and 6-311++G(3df,3pd) were used to perform calculations on H3O+...C2H2 and C2H3+...C2H2 complexes and related species. Hydrogen bonds existing for the analyzed complexes were investigated as well as related pi-H...O --> pi...H-O and pi-H...pi --> pi...H-pi proton-transfer processes. For some of the complexes analyzed the multicenter pi-H interaction possessing the properties of a covalent bond acts as a proton donor; more generally it is classified as the Lewis acid. The quantum theory of "atoms in molecules" (QTAIM) was also applied to deepen the nature of these interactions in terms of characteristics of bond critical points. The pi-H...O, O-H...pi, and pi-H...pi interactions analyzed here may be classified as hydrogen bonds since their characteristics are the same as or at least similar to those of typical hydrogen bonds. H...pi interactions are common in crystal structures of organic and organometallic compounds. The analyses performed here show a continuum of such interactions since there are H...pi contacts possessing the characteristics of weak intermolecular interactions on the one hand and pi-H multicenter covalent bonds on the other. Ab initio and QTAIM results support the latter statements.     

Theoretical study of binding interactions and vibrational Raman spectra of water in hydrogen-bonded anionic complexes: (H2O)n- (n = 2 and 3), H2O...X- (X = F, Cl, Br, and I), and H2O...M- (M = Cu, Ag, and Au)

Binding interactions and Raman spectra of water in hydrogen-bonded anionic complexes have been studied by using the hybrid density functional theory method (B3LYP) and ab initio (MP2) method. In order to explore the influence of hydrogen bond interactions and the anionic effect on the Raman intensities of water, model complexes, such as the negatively charged water clusters ((H2O)n-, n = 2 and 3), the water...halide anions (H2O...X-, X = F, Cl, Br, and I), and the water-metal atom anionic complexes (H2O...M-, M = Cu, Ag, and Au), have been employed in the present calculations. These model complexes contained different types of hydrogen bonds, such as O-H...X-, O-H...M-, O-H...O, and O-H...e-. In particular, the last one is a dipole-bound electron involved in the anionic water clusters. Our results showed that there exists a large enhancement in the off-resonance Raman intensities of both the H-O-H bending mode and the hydrogen-bonded O-H stretching mode, and the enhancement factor is more significant for the former than for the latter. The reasons for these spectral properties can be attributed to the strong polarization effect of the proton acceptors (X-, M-, O, and e-) in these hydrogen-bonded complexes. We proposed that the strong Raman signal of the H-O-H bending mode may be used as a fingerprint to address the local microstructures of water molecules in the chemical and biological systems.     

O-H...O interactions involving doubly charged anions: charge compression in carbonate-bicarbonate crystals

The O-H...O interaction formed by the anions HCO(3)(-) and CO(3)(2-) has been investigated on the basis of data retrieved from the Inorganic Crystal Structure Database (ICSD) and by means of ab initio computations. It has been shown that the O-H...O separations associated with HCO(3)(-)...(3)(2-) interactions are shorter than those found in crystals containing hydrogen carbonate monoanions such as HCO(3)(-)...HCO(3)(-). Ab initio MP2/6-311G++(2d,2p) computations on the crystal Na(3)(HCO(3))(CO(3)).2H(2)O have shown that the interaction between the monoanion donor and the dianion acceptor, for example HCO(3)(-)...CO(3)(2-), is more repulsive than that between singly charged ions, for example HCO(3)(-)...HCO(3)(-), but is largely overcompensated for by anion-cation electrostatic attractions. The shortening of the (-)O-H...O(2-) interaction relative to the (-)O-H...O(-) interaction has been explained as a consequence of the increased charge compression, that is of the stronger cation-anion interactions established by the CO(3)(2-) dianions with respect to those established by monoanions, and does not reflect an increase in the strength of the (-)O-H ...O(-) interaction. To expand the structural sample in the crystal packing analysis, the structure of the novel mixed salt K(2)Na(HCO(3))(CO(3)).2H(2)O has been determined by single-crystal X-ray diffraction and compared with the structure of the salt Na(3)(HCO(3))(CO(3)).2H(2)O used in the computations.     

Carboxylic acid clathrate hosts of Diels-Alder adducts of phencyclone and 2-alkenoic acids. Role of bidentate C-H ... O hydrogen bonds between the phenanthrene and carbonyl groups in host-host networks

Carboxylic acid host compounds (3) having a phenanthrene-condensed bicyclo[2.2.1]hept-2-en-7-one skeleton have been synthesized by the [4 + 2]pi cycloaddition of phencyclone (1a) with 2-alkenoic acids (2) and their inclusion behavior was investigated. The endo [4 + 2]pi cycloadducts (3) enclathrated alcohols and ethers besides aromatics and ketones. The X-ray crystallographic analysis of the inclusion compound (3ac-dioxane) of the endo [4 + 2]pi cycloadduct (3ac) of phencyclone and trans 2-butenoic acid (2c) indicated that dioxanes are located at the opposite side of the bridged carbonyl of the bicyclo[2.2.1]hept-2-en-7-one moiety, in which the O-H...O and C-H...O hydrogen bonds play an important role in the inclusion complex formation. Similarly, a pair of 3-pentanone molecules were included in the endo [4 + 2] pi cycloadduct (3ae) of 1a and cinnamic acid (2e). In both cases, the hosts are linked by the edge-to-face interaction between the phenanthrene and phenyl rings and the "bidentate" C-H...O hydrogen bonds between the phenanthrene-ring hydrogens and the bridged carbonyl or the carboxylic carbonyl group. The endo [4 + 2] pi cycloadduct (3bl) of tetracyclone (1b) and acrylamide (2l) also showed a wide-range inclusion behavior, in which alcohols are included by making a hydrogen-bond loop with the amide groups. The inclusion behavior of the carboxylic acid Diels-Alder hosts is discussed on the basis of the single crystal X-ray analysis, thermal analysis and semiempirical molecular orbital calculation data.     

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.     

Limitations of the molecular multipole expansion treatment of electrostatic interactions for C-H...O and O-H...O hydrogen bonds and application of a general charge density approach

A molecular multipole expansion treatment (up to hexadecapole) is examined for its accuracy in describing hydrogen-bond electrostatic interactions, with particular reference to explaining the differences between blue-shifted C-H...O and red-shifted O-H...O bonds. In interactions of H2O and CH4 with point charges at hydrogen-bonding distances, we find that the molecular multipole treatment not only fails to reproduce ab initio energies but also forces on OH or CH bonds, and therefore cannot properly account for the electrostatic component of the interaction. A treatment based on a molecule's permanent charge density and its derivatives and the charge density and its derivatives induced by an external multipole distribution is in full accord with ab initio results, as shown by application to models of the H2O-H2O and CH4-FH systems. Such a charge density approach provides a fundamental basis for understanding the importance of interaction forces in initiating structural change and thereby altering molecular properties.     

C—H...X (X = O,N or π) interactions in benzyl carbamate

The crystal packing and interaction energy of benzyl carbamate, C₈H₉NO₂, have been analysed in detail by the PIXEL method. Benzyl carbamate forms layers of hydrogen‐bonded molecules, with the layers connected by weaker C—H...π interactions. According to the PIXEL analysis, combinations of C—H...X (X = O, N or π) interactions are comparable in energy with hydrogen bonding. These interactions are necessary for explaining the geometry and the assembly of the layers.     

How to determine whether intramolecular H...H interactions can be classified as dihydrogen bonds

Different types of intramolecular H...H interactions have been analyzed using the MP2/6-311++G(d,p) level of approximation. These are C-H...H-B, C-H...H-Al, C-H...H-C, C-H...H-O, O-H...H-Al and O-H...H-B contacts. Quantum theory of atoms in molecules and natural bond orbitals methods were applied to better understand the nature of these interactions. It was found that some of the species analyzed possess the characteristics of typical hydrogen bonds, such as the O-H...O ones. The electron charge transfer from the Lewis base to the antibonding X-H (for example O-H) orbital of the Lewis acid is one such characteristic. The NBO method may be considered decisive to classify any system as dihydrogen bonded.     

Solution and solid-state models of peptide CH...O hydrogen bonds

Fumaramide derivatives were analyzed in solution by (1)H NMR spectroscopy and in the solid state by X-ray crystallography in order to characterize the formation of CH...O interactions under each condition and to thereby serve as models for these interactions in peptide and protein structure. Solutions of fumaramides at 10 mM in CDCl(3) were titrated with DMSO-d(6), resulting in chemical shifts that moved downfield for the CH groups thought to participate in CH...O=S(CD(3))(2) hydrogen bonds concurrent with NH...O=S(CD(3))(2) hydrogen bonding. In this model, nonparticipating CH groups under the same conditions showed no significant change in chemical shifts between 0.0 and 1.0 M DMSO-d(6) and then moved upfield at higher DMSO-d(6) concentrations. At concentrations above 1.0 M DMSO-d(6), the directed CH...O=S(CD(3))(2) hydrogen bonds provide protection from random DMSO-d(6) contact and prevent the chemical shifts for participating CH groups from moving upfield beyond the original value observed in CDCl(3). X-ray crystal structures identified CH...O=C hydrogen bonds alongside intermolecular NH...O=C hydrogen bonding, a result that supports the solution (1)H NMR spectroscopy results. The solution and solid-state data therefore both provide evidence for the presence of CH...O hydrogen bonds formed concurrent with NH...O hydrogen bonding in these structures. The CH...O=C hydrogen bonds in the X-ray crystal structures are similar to those described for antiparallel beta-sheet structure observed in protein X-ray crystal structures.     

Cooperativity between OH...O and CH...O hydrogen bonds involving dimethyl sulfoxide-H2O-H2O complex

The cooperativity between the O-H...O and C-H...O hydrogen bonds has been studied by quantum chemical calculations at the MP2/6-311++G(d,p) level in gaseous phase and at the B3LYP/6-311++G(d,p) level in solution. The interaction energies of the O-H...O and C-H...O H-bonds are increased by 53 and 58%, respectively, demonstrating that there is a large cooperativity. Analysis of hydrogen-bonding lengths, OH bond lengths, and OH stretching frequencies also supports such a conclusion. By NBO analysis, it is found that orbital interaction plays a great role in enhancing their cooperativity. The strength increase of the C-H...O H-bond is larger than that of the O-H...O H-bond due to the cooperativity. The solvent has a weakening effect on the cooperativity.     

1,2,4,5‐Tetrazines vs. Carboxylic Acid Dimers: Molecular Chemistry vs. Supramolecular Chemistry

The structures of six new tetrazines have been determined and their molecular packing has been compared to the supermolecular architecture observed in related carboxylic acid dimers. In the tetrazines, covalent N? N bonds are considered to replace the intermolecular O? H???O hydrogen bonds of the carboxylic acids. In the systems investigated, it is apparent that, in the majority of cases, the covalent six‐membered ring of the tetrazine is an appropriate replacement for the carboxylic acid synthon. This apparent interplay between molecular and supramolecular units may have applications in the crystal engineering of new materials.