Dimer or Catemer? Low-Energy Crystal Packings for Small Carboxylic Acids

Specific energy contributions from competing hydrogen-bonded structures in six polymorphs of phenobarbital

Background

In solid state structures of organic molecules, identical sets of H-bond donor and acceptor functions can result in a range of distinct H-bond connectivity modes. Specifically, competing H-bond structures (HBSs) may differ in the quantitative proportion between one-point and multiple-point H-bond connections. For an assessment of such HBSs, the effects of their internal as well as external (packing) interactions need to be taken into consideration. The semi-classical density sums (SCDS-PIXEL) method, which enables the calculation of interaction energies for molecule–molecule pairs, was used to investigate six polymorphs of phenobarbital (Pbtl) with different quantitative proportions of one-point and two-point H-bond connections.

Results

The structures of polymorphs V and VI of Pbtl were determined from single crystal data. Two-point H-bond connections are inherently inflexible in their geometry and lie within a small PIXEL energy range (−45.7 to −49.7 kJ mol⁻¹). One-point H-bond connections are geometrically less restricted and subsequently show large variations in their dispersion terms and total energies (−23.1 to −40.5 kJ mol⁻¹). The comparison of sums of interaction energies in small clusters containing only the strongest intermolecular interactions showed an advantage for compact HBSs with multiple-point connections, whereas alternative HBSs based on one-point connections may enable more favourable overall packing interactions (i.e. V vs. III). Energy penalties associated with experimental intramolecular geometries relative to the global conformational energy minimum were calculated and used to correct total PIXEL energies. The estimated order of stabilities (based on PIXEL energies) is III > I > II > VI > X > V, with a difference of just 1.7 kJ mol⁻¹ between the three most stable forms.

Conclusions

For an analysis of competing HBSs, one has to consider the contributions from internal H-bond and non-H-bond interactions, from the packing of multiple HBS instances and intramolecular energy penalties. A compact HBS based on multiple-point H-bond connections should typically lead to more packing alternatives and ultimately to a larger number of viable low-energy structures than a competing one-point HBS (i.e. dimer vs. catemer). Coulombic interaction energies associated with typical short intermolecular C–H···O contact geometries are small in comparison with dispersion effects associated with the packing complementary molecular shapes.Graphical abstract

A comprehensive classification and nomenclature of carboxyl-carboxyl(ate) supramolecular motifs and related catemers: implications for biomolecular systems

Carboxyl and carboxylate groups form important supramolecular motifs (synthons). Besides carboxyl cyclic dimers, carboxyl and carboxylate groups can associate through a single hydrogen bond. Carboxylic groups can further form polymeric-like catemer chains within crystals. To date, no exhaustive classification of these motifs has been established. In this work, 17 association types were identified (13 carboxyl-carboxyl and 4 carboxyl-carboxylate motifs) by taking into account the syn and anti carboxyl conformers, as well as the syn and anti lone pairs of the O atoms. From these data, a simple rule was derived stating that only eight distinct catemer motifs involving repetitive combinations of syn and anti carboxyl groups can be formed. Examples extracted from the Cambridge Structural Database (CSD) for all identified dimers and catemers are presented, as well as statistical data related to their occurrence and conformational preferences. The inter-carboxyl(ate) and carboxyl(ate)-water hydrogen-bond properties are described, stressing the occurrence of very short (strong) hydrogen bonds. The precise characterization and classification of these supramolecular motifs should be of interest in crystal engineering, pharmaceutical and also biomolecular sciences, where similar motifs occur in the form of pairs of Asp/Glu amino acids or motifs involving ligands bearing carboxyl(ate) groups. Hence, we present data emphasizing how the analysis of hydrogen-containing small molecules of high resolution can help understand structural aspects of larger and more complex biomolecular systems of lower resolution.

Crystal structure of the α-racemate of methohexital

Mol-ecules of the title compound, C14H18N2O3 [systematic name: 5-allyl-5-(hex-3-yn-2-yl)-1-methylpyrimidine-2,4,6(1H,3H,5H)-trione in the (RbSh )/(SbRh ) racemic form], are connected by mutual N-H⋯O=C hydrogen bonds in which the carbonyl group at the 2-position of the pyrimidine-trione ring is employed. These inter-actions result in an inversion dimer which displays a central R 2 (2)(8) ring motif. This dimer is topologically distinct from that of the previously reported (SbRh ) form, which is, however, also based on an R 2 (2)(8) motif. The methyl group at the 1-position of the pyrimidine-trione ring in the title structure is disordered over two sets of sites in a 0.57 (2):0.43 (2) ratio.

Effect of carboxylated poly(ethylene oxide-b-propylene oxide-b-ethylene oxide) block copolymer on nanostructured unsaturated polyester resin

A carboxylated poly(ethylene oxide-b-propylene oxide-b-ethylene oxide) (PEO-b-PPO-b-PEO) block copolymer was used to fabricate nanostructured unsaturated polyester materials.

Self-assembly of hydrogen-bonded two-dimensional quasicrystals

The process of molecular self-assembly on solid surfaces is essentially one of crystallization in two dimensions, and the structures that result depend on the interplay between intermolecular forces and the interaction between adsorbates and the underlying substrate. Because a single hydrogen bond typically has an energy between 15 and 35 kilojoules per mole, hydrogen bonding can be a strong driver of molecular assembly; this is apparent from the dominant role of hydrogen bonding in nucleic-acid base pairing, as well as in the secondary structure of proteins. Carboxylic acid functional groups, which provide two hydrogen bonds, are particularly promising and reliable in creating and maintaining surface order, and self-assembled monolayers of benzoic acids produce structure that depends on the number and relative placement of carboxylic acid groups. Here we use scanning tunnelling microscopy to study self-assembled monolayers of ferrocenecarboxylic acid (FcCOOH), and find that, rather than producing dimeric or linear structures typical of carboxylic acids, FcCOOH forms highly unusual cyclic hydrogen-bonded pentamers, which combine with simultaneously formed FcCOOH dimers to form two-dimensional quasicrystallites that exhibit local five-fold symmetry and maintain translational and rotational order (without periodicity) for distances of more than 400 ångströms.

Hydrogen-bond networks in polymorphs and solvates of metallorganic complexes containing ruthenium and aminoamide ligands

The hydrogen-bond networks of half-sandwich Ru(ii) complexes containing primary and secondary amide groups are described together with their guest inclusion properties.

Establishing the ellipsoidal geometry of a benzoic acid-based amphiphile via dimer switching: insights from intramolecular rotation and facial H-bond torsion

Soft molecular ellipsoids conceived from 3,4-di(dodecyloxy)benzoic acid (DDBA) amphiphile draw attention to monomer structure design, intramolecular -COOH headgroup twist (ϕ°) and cyclic-acyclic dimer switching through facial H-bond torsion (ψ°). Generically, precipitation in hydrogen bonded systems has been the prime phenomenon once the critical aggregation concentrations were reached in the bulk solution. DDBA was no exception to this generalization. It formed precipitates in chloroform and methanol with no specific geometry but with cyclic dimer motifs in them. On the contrary, surface pressure modulated interfacial aggregation with ellipsoidal geometry followed acyclic dimerization (catemer motif) with various levels of headgroup torsion, established through real-time polarization modulated infrared reflection-absorption spectroscopy (IRRAS) and density functional theory (DFT) calculations, that estimated the energy costs for these unexplored pathways. The reaction coordinates ϕ° and ψ° in consonance with 2D surface pressure modulation thus directed the shape anisotropy during the dynamic self-assembly of DDBA. Changes in subphase pH and metal ionic environment had a derogatory effect on the ellipsoid formation, the structural requirement for which strictly followed a stringent need for twin alkyl chains in an asymmetric unit cell, as 4-dodecyloxybenzoic acid (MABA) with a single alkyl chain formed exclusively spherical assemblies with no dimer modulation. The investigation thus reports unexplored energy pathways toward ellipsoidal geometry of the amphiphile in the course of its interfacial aggregation.

Role of hydrogen bonding on the self-organization of phenyleneethynylenes on surfaces

A series of carboxylic acid substituted phenyleneethynylenes, having a rigid backbone of 2.7 ± 0.1 nm, were synthesized by following the Heck-Cassar-Sonagashira-Hagihara cross-coupling reaction. Hydrogen bonding, through the formation of cyclic dimers of carboxylic acid, is more preferred over catemeric structures in all the molecular systems under investigation. The formation of extended two-dimensional patterns on highly oriented pyrolitic graphite (HOPG) surface is dictated by the position as well as number of the carboxylic acid groups on the phenyleneethynylenes. Highly ordered extended arrangements, in the linear and stepwise fashion, were observed when the carboxylic acid groups are attached in the para and meta positions of phenyleneethynylenes. The vital role of the number of carboxylic acid on the organization of molecules is evident in the case of tetracarboxylic acid derivative wherein a Kagome-type structure was observed. Further, the coassembly of two types of phenyleneethynylenes was achieved on HOPG surface through acid base interaction.

(±)-2,2-Dimethyl-5-oxotetrahydrofuran-3-carboxylic acid (terebic acid): a racemic layered structure

A racemic crystalline form of terebic acid, C7H10O4, which is an important industrial chemical compound, is reported for the first time. The crystal structure is stabilized by O—H...O and C—H...O hydrogen bonds which form racemic double layers parallel to (001).

The stability of the acetic acid dimer in microhydrated environments and in aqueous solution

The thermodynamic stability of the acetic acid dimer conformers in microhydrated environments and in aqueous solution was studied by means of molecular dynamics simulations using the density functional based tight binding (DFTB) method. To confirm the reliability of this method for the system studied, density functional theory (DFT) and second order Møller-Plesset perturbation theory (MP2) calculations were performed for comparison. Classical optimized potentials for liquid simulations (OPLS) force field dynamics was used as well. One focus of this work was laid on the study of the capabilities of water molecules to break the hydrogen bonds of the acetic acid dimer. The barrier for insertion of one water molecule into the most stable cyclic dimer is found to lie between 3.25 and 4.8 kcal mol(-1) for the quantum mechanical methods, but only at 1.2 kcal mol(-1) for OPLS. Starting from different acetic acid dimer structures optimized in gas phase, DFTB dynamics simulations give a different picture of the stability in the microhydrated environment (4 to 12 water molecules) as compared to aqueous solution. In the former case all conformers are converted to the hydrated cyclic dimer, which remains stable over the entire simulation time of 1 ns. These results demonstrate that the considered microhydrated environment is not sufficient to dissociate the acetic acid dimer. In aqueous solution, however, the DFTB dynamics shows dissociation of all dimer structures (or processes leading thereto) starting after about 50 ps, demonstrating the capability of the water environment to break up the relatively strong hydrogen bridges. The OPLS dynamics in the aqueous environment shows--in contrast to the DFTB results--immediate dissociation, but a similar long-term behavior.

Computational prediction of salt and cocrystal structures--does a proton position matter?

The lattice energy landscape is calculated for three pyridinium carboxylate salts and the corresponding pyridine·carboxylic acid cocrystals. Experimentally, one system crystallizes as a salt, another as a cocrystal and the acidic proton in the third is disordered across the N(arom)...O hydrogen bond vector. A novel structure of a 1:1 4-cyanopyridine·4-fluorobenzoic acid cocrystal (I) was characterized to provide the cocrystal as a system with an isolated carboxylic acid-pyridine heterosynthon. By contrast, the 4-dimethylaminopyridinium maleate salt (GUKVUE) shows the effects of an internal hydrogen bond, and the proton-disordered pyridine·isophthalic acid crystal (IYUPEX) shows the effects of competing intermolecular hydrogen bonds. All three crystal structures were found low in energy on the lattice energy landscape for the correct proton connectivity. For all three systems, comparing the salt and cocrystal energy landscapes shows the importance of the proton position for the relative stabilities of structures, despite the expected similarities between the ionized and neutral forms of the carboxylic acid-pyridine heterosynthon. The systems with additional hydrogen bonds have some hydrogen bonding motifs that are only favourable for the salt or for the cocrystal. This illustrates the sensitivity of the range of thermodynamically plausible crystal structures to whether the molecules are assumed to be ionized or neutral.

Modelling organic crystal structures using distributed multipole and polarizability-based model intermolecular potentials

Crystal structure prediction for organic molecules requires both the fast assessment of thousands to millions of crystal structures and the greatest possible accuracy in their relative energies. We describe a crystal lattice simulation program, DMACRYS, emphasizing the features that make it suitable for use in crystal structure prediction for pharmaceutical molecules using accurate anisotropic atom-atom model intermolecular potentials based on the theory of intermolecular forces. DMACRYS can optimize the lattice energy of a crystal, calculate the second derivative properties, and reduce the symmetry of the spacegroup to move away from a transition state. The calculated terahertz frequency k = 0 rigid-body lattice modes and elastic tensor can be used to estimate free energies. The program uses a distributed multipole electrostatic model (Q, t = 00,...,44s) for the electrostatic fields, and can use anisotropic atom-atom repulsion models, damped isotropic dispersion up to R(-10), as well as a range of empirically fitted isotropic exp-6 atom-atom models with different definitions of atomic types. A new feature is that an accurate model for the induction energy contribution to the lattice energy has been implemented that uses atomic anisotropic dipole polarizability models (alpha, t = (10,10)...(11c,11s)) to evaluate the changes in the molecular charge density induced by the electrostatic field within the crystal. It is demonstrated, using the four polymorphs of the pharmaceutical carbamazepine C(15)H(12)N(2)O, that whilst reproducing crystal structures is relatively easy, calculating the polymorphic energy differences to the accuracy of a few kJ mol(-1) required for applications is very demanding of assumptions made in the modelling. Thus DMACRYS enables the comparison of both known and hypothetical crystal structures as an aid to the development of pharmaceuticals and other speciality organic materials, and provides a tool to develop the modelling of the intermolecular forces involved in molecular recognition processes.

Crystal structure prediction from first principles

The prediction of structure at the atomic level is one of the most fundamental challenges in condensed matter science. Here we survey the current status of the field and consider recent developments in methodology, paying particular attention to approaches for surveying energy landscapes. We illustrate the current state of the art in this field with topical applications to inorganic, especially microporous solids, and to molecular crystals; we also look at applications to nanoparticulate structures. Finally, we consider future directions and challenges in the field.

Self-assembly of discotic mesogens in solution and in liquid crystalline phases: effects of substituent position and hydrogen bonding

The effects of functional group position on the phase behavior of discotic mesogens was examined for a series of dibenzophenazine derivatives bearing a carboxylic acid, methyl carboxylate, or nitro group. In all cases, changing the position of the group from the "top" to the "side" of the aromatic core led to dramatic differences in the phase behavior, both in terms of the stability of the liquid crystalline phases as well as the types of mesophases formed. For the non-hydrogen bonding ester and nitro derivatives, moving the substituent to the side of the core led to a lowering of the clearing temperatures or loss of liquid crystallinity. Carboxylic acid derivatives exhibit broad mesophases irrespective of the position of the acid group, but mesogens bearing this group on the side of the core exclusively form Col(h) phases, whereas those with an acid group on the top of the core exhibit more varied mesomorphism, with the formation of Col(h), Col(r), and nematic phases. Contrary to expectations, the presence of a carboxylic acid group on the side of the core does not appear to lead to the formation of dimeric structures in the liquid crystalline phase, although the columnar structures appear to be stabilized by intermolecular hydrogen bonding along the columns. These derivatives also form pi-stacked dimers in solution; the structure of these dimers are consistent with the proposed structure of the columnar phases.

Packing modes in some mono- and disubstituted phenylpropiolic acids: repeated occurrence of the rare syn,anti catemer

The catemer is an infinite one-dimensional pattern formed by the carboxylic acid group in crystals, and is constituted with O-H...O hydrogen bonds. The catemer is uncommon and may be contrasted with the ubiquitous carboxylic acid dimer, the favored mode of association of this functional group. Both catemers and dimers, however, have two O-H...O hydrogen bonds for each carboxy group, so the reasons for the rarity of the catemer must lie elsewhere. In this paper, we describe a group of around 25 phenylpropiolic acids in which the catemer is the default packing mode. Exceptionally, the particular catemer that is found in this family is of the very rare syn,anti variety. We show that a necessary ingredient in catemer formation is a supportive C-H...O hydrogen bond from a proximal C-H group, which is located on the phenyl ring, ortho to the ethynyl group, and suitably activated by electron withdrawing substituents. When steric factors become noteworthy, alternative patterns are adopted, such as the syn,syn catemer and, in one case, a rare cisoid dimer. When electron-donating groups, either through inductive effect such as methyl or through resonance such as halogens, are present on the phenyl ring, the dimer is formed in all but one case. Polymorphism seems not to be an issue in these carboxylic acids in that no compound would generally crystallize as both a dimer and a catemer. It may be concluded that a supporting interaction, in this case a C-H...O hydrogen bond, is the essential condition for the formation of any carboxylic acid catemer. Catemers are so rare because it is difficult to set up this type of supporting interaction in most carboxylic acids.

Determination of the Conformation of 2-Hydroxy- and 2-Aminobenzoic Acid Dimers Using 13C NMR and Density Functional Theory/Natural Bond Order Analysis: The Central Importance of the Carboxylic Acid Carbon

The 13C chemical shift for the carboxylic acid carbon provides a powerful diagnostic probe to determine the preferred isomeric dimer structures of benzoic acid derivatives undergoing intra- and intermolecular H-bonding in the gas, solution and crystalline phases. We have employed hybrid density functional calculations and natural bond orbital analysis to elucidate the electronic origins of the observed 13C shieldings and their relationship to isomeric stability. We find that delocalizing interactions from the carbonyl oxygen lone pairs (nO) into vicinal carbon-oxygen and carbon-carbon antibonds (sigmaCO*,sigmaCC*) make critical contributions to the 13C shieldings, and these nO --> sigmaCO*, nO --> sigmaCC* interactions are in turn sensitive to the intramolecular interactions that dictate dimer structure and stability. The carboxyl carbon atom can thus serve as a useful detector of subtle structural and conformational features in this pharmacologically important class of carboxylic acid interactions.

Sodium Cation Affinities of MALDI Matrices Determined by Guided Ion Beam Tandem Mass Spectrometry: Application to Benzoic Acid Derivatives†

Threshold collision-induced dissociation of Na(+)(xBA) complexes with Xe is studied using guided ion beam mass spectrometry. The xBA ligands studied include benzoic acid and all of the mono- and dihydroxy-substituted benzoic acids: 2-, 3-, and 4-hydroxybenzoic acid and 2,3-, 2,4-, 2,5-, 2,6-, 3,4-, and 3,5-dihydroxybenzoic acid. In all cases, the primary product corresponds to endothermic loss of the intact xBA ligand. The cross section thresholds are interpreted to yield 0 and 298 K bond dissociation energies (BDEs) for Na(+)-xBA after accounting for the effects of multiple ion-neutral collisions, internal and kinetic energy distributions of the reactants, and dissociation lifetimes. Density functional theory calculations at the B3LYP/6-31G* level of theory are used to determine the structures of these complexes and provide the molecular constants necessary for the thermodynamic analysis of the experimental data. Theoretical BDEs are determined at the B3LYP/6-311+G(2d,2p) and MP2(full)/6-311+G(2d,2p) levels using the B3LYP/6-31G* optimized geometries. The trends in the measured BDEs suggest two very different binding modes for the Na(+)(xBA) complexes, while theory finds four. In general, the most stable binding conformation involves the formation of a six-membered chelation ring via interaction with the carbonyl and 2-hydroxyl oxygen atoms. The ground state geometries of the Na(+)(xBA) complexes in which the ligand does not possess a 2-hydroxyl group generally involve binding of Na(+) to either the carbonyl oxygen atom or to both oxygen atoms of the carboxylic acid group. These binding modes tend to be competitive because the enhancement in binding associated with the chelation interactions in the latter is mediated by steric repulsion between the hydroxyl and ortho hydrogen atoms. When possible, hydrogen bonding interactions with the ring hydroxyl group(s) enhance the stability of these complexes. The agreement between the theoretical and experimental BDEs is quite good for B3LYP and somewhat less satisfactory for MP2(full).

Aggregation of acetic and propionic acid in argon matrices--a matrix isolation and computational study

Monomeric acetic acid MA and propionic acid MP were isolated in argon matrices at 10K by using a pulse deposition technique. The dimerization of the monomers was induced by warming the matrices from 10 to 40 K. Under these conditions the diffusion of small trapped molecules is rapid and the dimerization could be monitored directly by IR spectroscopy. Both carboxylic acids form the symmetrical dimers B with two strong C=O...HO hydrogen bridges as the thermodynamically most stable dimers. With acetic acid a less stable dimer AA could be obtained if high concentrations of acetic acid in argon were used during the deposition of the matrix. On annealing this dimer rearranges to the more stable BA. In contrast, propionic acid does not form a corresponding less stable dimer under any experimental condition. These observations are rationalized on the basis of DFT and ab initio calculations.

Crystal structure predictions using five space groups with two independent molecules. The case of small organic acids

Crystal structure generations with two independent molecules have been performed for a series of carboxylic acids, using a slightly modified version of the OPLS force field. It was found that in this way the experimental structures with one independent molecule were produced as special cases, except for the molecules with four or more internal degrees of freedom. This work shows that a search with two independent molecules in only five space groups, although costly in computer power, can automatically also find structures with one independent molecule in many supergroups. Considering the observed abundances of structural classes, such a search should cover more than 95% of the possible homomolecular crystal structures.