Hydrogen-bonded Carboxylic Acid Dimers Research Articles

(η5-Carb-oxy-cyclo-penta-dien-yl)(η7-cyclo-hepta-trien-yl)manganese(I) hexa-fluorido-phosphate.

The title compound, [Mn(C7H7)(C6H5O2)]PF6 or [(Cht)Mn(Cp'CO2H)]PF6, with Cht = cyclo-hepta-trienyl and Cp' = C5H4, is an air-stable, purple, heteroleptic, cationic sandwich complex with manganese in oxidation state +I and π-coordinating cyclo-hepta-trienyl and cyclo-penta-dienyl ligands. The latter ligand carries the carb-oxy-lic acid functionality. This 'tromancenium-8-carb-oxy-lic acid' with hexa-fluorido-phosphate as counter-ion represents a rare case of a cationic carb-oxy-lic acid. Structurally, this organometallic carb-oxy-lic acid displays the common motif of planar Osp 2⋯H-Osp 3/Osp 3-H⋯Osp 2 hydrogen-bonded carb-oxy-lic acid dimers with anti-oriented metallocenyl moieties, the cationic charge of which is balanced by octa-hedrally shaped hexa-fluorido-phosphate anions. Positional disorder is observed in the cyclo-hepta-trienyl ring and the PF6 - anion.

Glutathione Self-Assembles into a Shell of Hydrogen-Bonded Intermolecular Aggregates on "Naked" Silver Nanoparticles.

A detailed understanding of the molecular structure in nanoparticle ligand capping layers is crucial for their efficient incorporation into modern scientific and technological applications. Peptide ligands render the nanoparticles as biocompatible materials. Glutathione, a γ-ECG tripeptide, self-assembles into aggregates on the surface of ligand-free silver nanoparticles through intermolecular hydrogen bonding and forms a few nanometer-thick shells. Two-dimensional nonlinear infrared (2DIR) spectroscopy suggests that aggregates adopt a conformation resembling the β-sheet secondary structure. The shell thickness was evaluated with localized surface plasmon resonance spectroscopy and X-ray photoelectron spectroscopy. The amount of glutathione on the surface was obtained with spectrophotometry of a thiol-reactive probe. Our results suggest that the shell consists of ∼15 stacked molecular layers. These values correspond to the inter-sheet distances, which are significantly shorter than those in amyloid fibrils with relatively bulky side chains, but are comparable to glycine-rich silk fibrils, where the side chains are compact. The tight packing of the glutathione layers can be facilitated by hydrogen-bonded carboxylic acid dimers of glycine and the intermolecular salt bridges between the zwitterionic γ-glutamyl groups. The structure of the glutathione aggregates was studied by 2DIR spectroscopy of the amide-I vibrational modes using 13C isotope labeling of the cysteine carbonyl. Isotope dilution experiments revealed the coupling of modes forming vibrational excitons along the cysteine chain. The coupling along the γ-glutamyl exciton chain was estimated from these values. The obtained coupling strengths are slightly lower than those of native β-sheets, yet they appear large enough to point onto an ordered conformation of the peptides within the aggregate. Analysis of the excitons' anharmonicities and the strength of the transition dipole moments generally is in agreement with these observations.

Structural Elucidation of Enantiopure and Racemic 2-Bromo-3-Methylbutyric Acid

Halogenated carboxylic acids have been important compounds in chemical synthesis and indispensable research tools in biochemical studies for decades. Nevertheless, the number of structurally characterized simple α-brominated monocarboxylic acids is still limited. We herein report the crystallization and structural elucidation of (R)- and rac-2-bromo-3-methylbutyric acid (2-bromo-3-methylbutanoic acid, 1) to shed light on intermolecular interactions, in particular hydrogen bonding motifs, packing modes and preferred conformations in the solid-state. The crystal structures of (R)- and rac-1 are revealed by X-ray crystallography. Both compounds crystallize in the triclinic crystal system with Z = 2; (R)-1 exhibits two crystallographically distinct molecules. In the crystal, (R)-1 forms homochiral O–H···O hydrogen-bonded carboxylic acid dimers with approximate non-crystallographic C2 symmetry. In contrast, rac-1 features centrosymmetric heterochiral dimers with the same carboxy syn···syn homosynthon. The crystal packing of centrosymmetric rac-1 is denser than that of its enantiopure counterpart (R)-1. The molecules in both crystal structures adopt a virtually identical staggered conformation, despite different crystal environments, which indicates a preferred molecular structure of 1. Intermolecular interactions apart from classical O–H···O hydrogen bonds do not appear to have a crucial bearing on the solid-state structures of (R)- and rac-1.

N-Tosyl-L-proline benzene hemisolvate: a rare example of a hydrogen-bonded carboxylic acid dimer with symmetrically disordered H atoms.

The carboxylic acid group is an example of a functional group which possess a good hydrogen-bond donor (-OH) and acceptor (C=O). For this reason, carboxylic acids have a tendency to self-assembly by the formation of hydrogen bonds between the donor and acceptor sites. We present here the crystal structure of N-tosyl-L-proline (TPOH) benzene hemisolvate {systematic name: (2S)-1-[(4-methylbenzene)sulfonyl]pyrrolidine-2-carboxylic acid benzene hemisolvate}, C12H15NO4S·0.5C6H6, (I), in which a cyclic R22(8) hydrogen-bonded carboxylic acid dimer with a strong O-(1/2H)...(1/2H)-O hydrogen bond is observed. The compound was characterized by single-crystal X-ray diffraction and NMR spectroscopy, and crystallizes in the space group I2 with half a benzene molecule and one TPOH molecule in the asymmetric unit. The H atom of the carboxyl OH group is disordered over a twofold axis. An analysis of the intermolecular interactions using the noncovalent interaction (NCI) index showed that the TPOH molecules form dimers due to the strong O-(1/2H)...(1/2H)-O hydrogen bond, while the packing of the benzene solvent molecules is governed by weak dispersive interactions. A search of the Cambridge Structural Database revealed that the disordered dimeric motif observed in (I) was found previously only in six crystal structures.

Conformational dimorphism in o-nitrobenzoic acid: alternative ways to avoid the O...O clash.

Polymorphism is a challenging phenomenon and the competitive packing alternatives which are characteristic for polymorphs may be encountered for essentially rigid molecules. A second crystal form of the well known compound o-nitrobenzoic acid, C7H5NO4, an important intermediate in the production of dyes, pharmaceuticals and agrochemicals, is described. Although obtained serendipitously, its intra- and intermolecular features match expectations from database searches and theoretical calculations. O-H...O hydrogen-bonded carboxylic acid dimers represent the building blocks in both polymorphs. For steric reasons and in agreement with a calculated potential energy surface, the carboxylic acid and nitro groups cannot simultaneously be coplanar with the benzene ring but have to tilt. In the well established crystal form, this out-of-plane torsion is more pronounced for the nitro substituent. In contrast, the new polymorph is characterized by a major tilt of the carboxylic acid group. The molecules in both alternative crystal forms achieve a similar compromise with respect to acceptable intramolecular O...O contacts.

NEXAFS and XPS of p-Aminobenzoic Acid Polymorphs: The Influence of Local Environment

Nitrogen K-edge XPS and NEXAFS of the two polymorphic forms of para- aminobenzoic acid (PABA) are significantly different reflecting variation in hydrogen bonding. Alteration in hydrogen bonding at the amino group leads to a shift to high energy for both the XPS N 1s core level and the 3π* NEXAFS resonance with β-PABA. Participation of the amine group in the aromatic system causes the 1π* resonance to be sensitive to the nature of the intermolecular bonding at the para-carboxylic acid group, and a shift to low energy for α- PABA is observed due to hydrogen-bonded carboxylic acid dimer formation. FEFF calculations also successfully reproduce both the energy and intensity variations observed for the σ* shape resonance associated with the C-N bond, with the majority of the decrease in energy observed for b-PABA arising from the longer C-N bond.

Towards an understanding of the nucleation of alpha-para amino benzoic acid from ethanolic solutions: a multi-scale approach.

The molecular assembly and subsequent nucleation of para-amino benzoic acid (PABA) from ethanolic solutions is probed using a multi-scale and multi-technique approach. This is applied by examining and interrelating information regarding the molecular, solution-state, cluster, solid-state and surface structures to understand why the alpha form of PABA is crystallised in preference to its low temperature beta form. Calculations suggest that conformational changes within the solute molecule play little or no role in directing the nucleation of either the alpha or beta crystal forms. Combined ab initio and molecular dynamics calculations of the stability of small clusters in solution suggests that the hydrogen-bonded carboxylic acid dimers, present in the alpha structure, are the most stable in solution and play a major role in the self-assembly and polymorphic expression of the alpha form in ethanol in preference to the beta form. These calculations are in good agreement with X-ray small-angle scattering analysis which reveals the presence of PABA clusters in ethanol which are consistent with the size and shape of a carboxylic acid dimer. SAXS studies also reveal the presence of larger cluster structures in a size range 10-40 nm which appear to grow, perhaps reflecting a change in the balance between monomers and dimers within the solution during the nucleation process. The results of crystallisation-kinetics experiments indicate an instantaneous nucleation mechanism where the number of instantaneously nucleated crystallites is calculated to be 1360-660 nuclei per ml and the subsequent growth is found to be only rate limited by diffusion of the growth unit to the crystallite surface. A linear dependence of growth rate with respect to supersaturation is observed for the (0 1 -1) capping face, which is associated with strong π-π stacking interactions. This is consistent with a solid-on-solid mechanism associated with surface roughened growth and concomitant poor lattice-perfection. Conversely, the side (1 0 -1) surface has a growth mechanism consistent with a 2D nucleation birth and spread mechanism. Hence, these mechanisms result in very fast growth along the b-axis and the needle-like morphology that is observed for alpha-PABA.

Self-assembly of discrete and polymeric metallosupramolecular architectures from cyclen-derived ligands

Two divergent ligands 1,4,7,10-tetrakis-(4-cyanobenzyl)-1,4,7,10-tetraazacyclododecane L1 and 1,4,7,10-tetrakis-(4-carboxybenzyl)-1,4,7,10-tetraazacyclododecane dihydrochloride dihydrate H6L2·2Cl·2H2O have been prepared and structurally characterised, and the solid-state structures of four new metal complexes have been elucidated. Ligand L1 was found to form a dimeric complex of the form [Ag2(L1)2]·2ClO4 when reacted with silver perchlorate, in which a macrocycle-bound Ag(I) ion is coordinated by the nitrile group of an adjacent ligand, forming a tightly-bound pair of Ag(I) ions supported by intramolecular π–π interactions. Compound H6L2·2Cl·2H2O was prepared by a solvothermal recrystallization following hydrolysis of the ester precursor, and forms a densely packed three-dimensional structure containing numerous hydrogen bonding interactions. Complexes [Ni(H4L2)Cl]2·[NiCl4]·2EtOH 2 and [Co(H4L2)Cl]2·[CoCl4]·2EtOH 3 were characterised as isostructural discrete macrocycle-bound Ni(II) and Co(II) species where the formation of rare hydrogen-bonded carboxylic acid tetramers gives rise to a series of 2-dimensional sheets, containing checkerboard-type cavities encapsulating alternating tetrachloridometallate anions and regions containing disordered solvent molecules. Complex poly-{[Cu2Cl(H2L1)(HOEt)]2·[CuCl4]·5H2O} 4 consists of a series of two-dimensional sheets formed from a macrocycle-bound CuCl species linked by copper paddlewheel clusters and hydrogen-bonded carboxylic acid dimers. Charge balance is again achieved by tetrachloridometallate anions, and the sheets undergo parallel 2D → 2D interpenetration. The influence of the flexible geometry and donor ability of the methylene-linked pendant arms is clearly visible when comparing discrete complex 1 with hydrogen-bonded networks 2 and 3 and polymeric species 4. The presence of tetrachloridometallate counterions resulting from the presence of excess chloride ions in the reaction mixtures also provides powerful structure-directing effects in complexes 2, 3 and 4.

Cyclic Imide and Open-Chain Amide Carboxylic Acid Derivatives from the Facile Reaction of cis-Cyclohexane-1,2-Dicarboxylic Anhydride with Three Substituted Anilines

The structures of the compounds from the reaction of cis-cyclohexane-1,2-dicarboxylic anhydride with 4-chloroaniline [rac-2-[(4-chlorophenyl)carbamoyl]-cis-cyclohexane-1-carboxylic acid] (1), 4-bromoaniline [2-(4-bromophenyl)-3a,4,5,6,7,7a-hexahydroisoindole-1,3-dione] (2) and 3-carboxy-4-hydoxyaniline (5-aminosalicylic acid) [2-(3-carboxy-4-hydroxyphenyl)- 3a,4,5,6,7,7a-hexahydroisoindole-1,3-dione] (3) have been determined at 200 K. Crystals of the open-chain amide carboxylic acid 1 are orthorhombic, space group Pbcn, with unit cell dimensions a = 20.1753(10), b = 8.6267(4), c = 15.9940(9) Å, and Z = 8. Compounds 2 and 3 are cyclic imides, with 2 monoclinic having space group P21 and Z = 4, with cell dimensions a = 11.5321(3), b = 6.7095(2), c = 17.2040(5) Å, β = 102.527(3)°. Compound 3 is orthorhombic, space group P212121 with Z = 4 and cell dimensions a = 6.4642(3), b = 12.8196(5), c = 16.4197(7) Å. Molecules of 1 form hydrogen-bonded cyclic carboxylic acid dimers [graph set R 2 2 (8)] which are extended into a two-dimensional layered structure through amide-group associations: 3 forms into one-dimensional zigzag chains through carboxylic acid···imide O-atom hydrogen bonds, while compound 2 is essentially unassociated. With both cyclic imides 2 and 3, disorder is found which involves the presence of partial enantiomeric replacement of the cis-1,2-substituted cyclohexane ring systems. The structures of an open-chain amide carboxylic acid and two cyclic imides from the facile reaction of cis-cyclohexane-1,2-dicarboxylic acid anhydride with the 4-chloro-, 4-bromo- and 3-carboxy-4-hydroxyaniline, respectively, are reported together with their hydrogen-bonding patterns

Little change but great effect: varying supramolecular interactions in 2,5-dimethoxyterephthalic acid and 2,5-diethoxyterephthalic acid

The title terephthalic acid derivatives, namely 2,5-dimethoxyterephthalic acid, C(10)H(10)O(6), (I), and 2,5-diethoxyterephthalic acid, C(12)H(14)O(6), (II), exhibit nearly planar molecular structures, with maximum deviations from the least-squares planes calculated for all non-H atoms of 0.0418 (6) and 0.0902 (10) Å for (I) and (II), respectively. The molecules of both title compounds contain an inversion centre and thus the asymmetric unit of both crystal structures consists of only half a molecule. It is a remarkable fact that a comparatively small change in the substitution of the terephthalic acid [dimethoxy in (I) versus diethoxy in (II)] causes major differences in the dominating supramolecular interactions. While in (II) the packing structure is stabilized by typical intermolecular hydrogen-bonded carboxylic acid dimer interactions, the carboxyl group in (I) forms an unusual intramolecular hydrogen bond with the O atom of the neighbouring methoxy group.

Two-Dimensional Infrared Spectroscopy of Intermolecular Hydrogen Bonds in the Condensed Phase

Hydrogen bonding plays a key role in the structural, physical, and chemical properties of liquids such as water and in macromolecular structures such as proteins. Vibrational spectroscopy is an important tool for understanding hydrogen bonding because it provides a way to observe local molecular geometries and their interaction with the environment. Linear vibrational spectroscopy has mapped characteristic changes of vibrational spectra and the occurrence of new bands that form upon hydrogen bonding. However, linear vibrational spectroscopy gives very limited insight into ultrafast dynamics of the underlying molecular interactions, such as the motions of hydrogen-bonded groups, energy dissipation and delocalization, and the fluctuations within hydrogen-bonded structures that occur in the ultrafast time domain. Nonlinear vibrational spectroscopy with its femtosecond time resolution can discern these dynamic processes in real time and has emerged as an important tool for unraveling molecular dynamics and for quantifying interactions that govern the vibrational and structural dynamics of hydrogen bonds. This Account reviews recent progress originating from third-order nonlinear methods of coherent multidimensional vibrational spectroscopy. Ultrafast dynamics of intermolecular hydrogen bonds are addressed for a number of prototype systems: hydrogen-bonded carboxylic acid dimers in an aprotic liquid environment, the disordered fluctuating hydrogen-bond network of liquid water, and DNA oligomers interacting with water. Cyclic carboxylic acid dimers display a rich scheme of vibrational couplings, resulting in OH stretching absorption bands with highly complex spectral envelopes. Two-dimensional spectroscopy of acetic acid dimers in a nonpolar liquid environment demonstrates that multiple Fermi resonances of the OH stretching mode with overtones and combination tones of fingerprint vibrations dominate both the 2D and linear absorption spectra. The coupling of the OH stretching mode with low-frequency hydrogen-bonding modes leads to additional progressions and coherent low-frequency hydrogen-bond motions in the subpicosecond time domain. In water, the 2D spectra reveal ultrafast spectral diffusion on a sub-100 fs time scale caused by the ultrafast structural fluctuations of the strongly coupled hydrogen-bond network. Librational motions play a key role for the ultrafast loss of structural memory. Spectral diffusion rates are enhanced by resonant transfer of OH stretching quanta between water molecules, typically occurring on a 100 fs time scale. In DNA oligomers, femtosecond nonlinear vibrational spectroscopy resolves NH and OH stretching bands in the highly congested infrared spectra of these molecules, which contain alternating adenine-thymine pairs. Studies at different levels of hydration reveal the spectral signatures of water molecules directly interacting with the phosphate groups of DNA and of a second water species forming a fluctuating environment around the DNA oligomers. We expect that the application of 2D infrared spectroscopy in an extended spectral range will reveal the intrinsic coupling between water and specific functional units of DNA.

An explanation for the high stability of polycarboxythiophenes in photovoltaic devices—A solid-state NMR dipolar recoupling study

Continuous operation of a polymer photovoltaic device under accelerated conditions for more than 1 year has been demonstrated (8760 h at 72 °C, 1000 W m −2, AM1.5, under vacuum). Formation of hydrogen-bonded networks is proposed to be responsible for the long lifetime and high stability observed in photovoltaic devices employing polythiophene substituted with carboxylic-acid moieties under oxygen free conditions. 1H and 13C solid-state NMR, IR, and ESR spectroscopy of unmodified and isotopically labeled polythiophenes were studied. Distances between the isotopically labeled carboxylic acid carbon atoms were measured by 13C solid-state magic-angle-spinning (MAS) NMR using symmetry-based double-quantum (2Q) dipolar recoupling. This revealed the presence of 13C– 13C distances of 3.85 Å, which correspond to the C–C distance in hydrogen-bonded carboxylic acid dimers. In spite of the presence of carboxylic groups in the polymer as demonstrated by 13C CP/MAS NMR and IR spectroscopy, the absence of carboxylic protons in solid state 1H NMR spectra indicate that they are mobile. We link the extraordinary stability of this system to the rigid nature, cross-linking through a hydrogen-bonded network and a partially oxidized state.

Rac-2-Hydroxy-2-(2-nitrophenyl)acetic acid

In the racemic title compound, C8H7NO5, the nitro group attached to the 2-hydroxy­acetic acid (glycolic acid) moiety is tilted by 31.2 (2)° with respect to the aromatic plane. The characteristics of the mol­ecular packing are (i) hydrogen-bonded carboxylic acid dimers; (ii) a trifurcated hydrogen bond with the 2-hydr­oxy function as the donor and a nitro O atom as the only inter­molecular acceptor, both kinds of hydrogen bonds linking the mol­ecules into ribbons along [001].

Co-Crystals of Caffeine and Hydroxy-2-naphthoic Acids: Unusual Formation of the Carboxylic Acid Dimer in the Presence of a Heterosynthon

A group of caffeine-containing co-crystals of hydroxy-2-naphthoic acids were synthesized and analyzed via single-crystal X-ray diffraction and IR analysis. The imidazole-carboxylic acid synthon was observed in co-crystals involving 1-hydroxy-2-naphthoic and 3-hydroxy-2-naphthoic acid. In the case of 6-hydroxy-2-naphthoic acid, the co-crystal exhibits a hydrogen-bonded carboxylic acid dimer in the presence of a hydroxyl-caffeine heterosynthon.

6-(2-Chloroacetamido)hexanoic acid

Crystals of the title compound, C 8 H 14 ClNO 3 , belong to the space group Cc and are characterized by an asymmetric unit containing two molecules, both with a twisted conformation. The molecular packing is stabilized by N-H···O=C hydrogen bonds between the amide groups of molecules with the same conformation. In addition, hydrogen-bonded cyclic carboxylic acid dimers are established between molecules with a different conformation. The ClCH 2 -CONH bond has a cis conformation in order to favour an intramolecular Cl···HN electrostatic interaction. Weak intra- and intermolecular CH 2 ···O=C interactions are also present.

2,3-Methylenedioxybenzoic acid

The title compound, C8H6O4, consists of a cyclic diether fused to benzoic acid and crystallizes as a hydrogen-bonded carboxylic acid dimer.

Bis(nateglinide) hydronium chloride, and its unique self-assembly into extended polymeric arraysviaO—H...O, N—H...Cl and O—H...Cl hydrogen bonds

The title compound, bis[(-)-N-(trans-4-isopropylcyclohexanecarbonyl)-D-phenylalanine] hydronium chloride, 2C19H27NO3.H3O+.Cl-, at 110 K contains four conformationally dissimilar moieties in the asymmetric unit, which are seemingly necessary in order to optimize the supramolecular association. The organic molecule forms O-H...O hydrogen-bonded carboxylic acid dimers, which are paired into six-component clusters via N-H...Cl hydrogen bonds through the two bridging chloride anions. These combined hexameric aggregates are further interlinked into extended two-dimensional network arrays via the hydronium ions by O-H...O and O-H...Cl hydrogen bonds. This study represents the first crystallographic report of nateglinide.

3,4,5-Triethoxybenzoic acid benzene solvate: An example of hydrogen-bonded carboxylic acid dimer

Crystals of 3,4,5-triethoxybenzoic acid benzene solvate, 3,4,5-(C2H5O)3C6H2COOH⋅ 0.25C6H6, are monoclinic, space group P2/c, with the cell dimensions at 100 K: a = 18.729(3), b = 10.6475(17), c = 14.390(2) A, β = 98.410(2)∘, V = 2838.7(8) A3, and Z = 8, Z′ = 2. In the crystal structure two symmetrically independent molecules of 3,4,5-triethoxybenzoic acid form a planar dimer by two O–H⋅sO hydrogen bonds.

Intermolecularly associated carboxylic acid dimers in the supramolecular assembly of 2-(2-phenylethyl)benzoic acid

The molecular structure of the title acid, $C_{15}H_{14}O_{2}$, exhibits a trans-planar arrangement of the aromatic rings. The carboxyl group is inclined at an angle of $6.4 (1) ^o$ with respect to the attached benzene ring. The classical hydrogen-bonded carboxylic acid dimers (O...O = 2.7 \AA), characterized by an $R^{2}_ 2(8)$ pattern, predominantly stabilize the supramolecular assembly.

2-Phenoxybenzoic acid at room temperature

In the crystal structure of the title compound, C13H10O3, the mol­ecules form classical hydrogen-bonded carboxylic acid dimers [O⋯O = 2.651 (2) A]. These dimers are linked by C—H⋯π and π–π inter­actions to give a three-dimensional network.