Hydrogen-bonded Cyclic Dimers Research Articles

Solid-state and solution-state self-association of dimethylarsinic acid: IR, NMR and theoretical study

The structure of dimethylarsinic acid (Me2AsOOH, DMA) in crystal and in solution in aprotic medium was studied by X-ray, spectroscopic (IR, NMR and Raman) and quantum chemical calculation (DFT) methods. Two polymorphs of DMA – hydrogen-bonded cyclic dimers or infinite chains – were obtained by growing crystals from protic and aprotic solvents. By comparison of the experimental data with the results of quantum-chemical calculations performed with periodic boundary conditions we propose ways how to distinguish two polymorphs using IR marker bands. The self-association of DMA in polar aprotic solution was studied by low-temperature NMR (T = 100 K, solvent CDF3/CDF2Cl mixture). By using H/D isotope effects on 1H NMR chemical shifts (appearing after a partial deuteration of DMA in the mobile proton sites) we were able to prove that in solution DMA forms cyclic dimers with two equivalent strong hydrogen bonds (in contrast, for example, to Me2POOH acid, which forms predominantly cyclic trimers). Based on the available IR spectra, the type of complexation does not change when the aprotic solvent is varied.

2-(2-Isopropylphenoxy)acetic acid

In the title compound, C11H14O3, the pendant –OCH2COOH chain is in an extended conformation and almost lies in the plane of the benzene ring, as indicated by the dihedral angle of 2.61 (5)°. In the crystal, molecules are linked by a pair of O—H...O hydrogen bonds, forming classical carboxylic acid inversion dimers, with an R 2 2(8) loop. The crystal structure of this compound have been reported previously [Smith et al. (1992). Aust. J. Chem. 45, 1101–1108], however, in that report, the unit-cell dimensions differ significantly from those of the title structure and the carboxyl H atom was disordered within a cyclic hydrogen-bonded dimer.

Crystal structures of the two epimers from the unusual thermal C6-epimerization of 5-oxo-1,2,3,5,5a,6,7,9b-octa-hydro-7,9a-ep-oxy-pyrrolo-[2,1-a]iso-indole-6-carb-oxy-lic acid, 5a(RS),6(SR),7(RS),9a(SR),9b(SR) and 5a(RS),6(RS),7(RS),9a(SR),9b(SR).

The isomeric title compounds, C12H13NO4 (Ia) and C12H13NO4 (IIa), the products of an usual thermal C6-epimerization of 5-oxo-1,2,3,5,5a,6,7,9b-octa-hydro-7,9a-ep-oxy-pyrrolo-[2,1-a]iso-indole-6-carb-oxy-lic acid, represent the two different diastereomers and have very similar mol-ecular geometries. The mol-ecules of both compounds comprise a fused tetra-cyclic system containing four five-membered rings (pyrrolidine, pyrrolidinone, di-hydro-furan and tetra-hydro-furan), all of which adopt the usual envelope conformations. The dihedral angle between the basal planes of the pyrrolidine and pyrrolidinone rings are 14.3 (2) and 16.50 (11)°, respectively, for (Ia) and (IIa). The nitro-gen atom has a slightly pyramidalized geometry [bond-angle sum = 355.9 and 355.3°, for (Ia) and (IIa)], respectively. In the crystal of (Ia), mol-ecules form zigzag-like hydrogen-bonded chains along [010] through strong O-H⋯O hydrogen bonds and are further linked by weak C-H⋯O hydrogen bonds into complex two-tier layers parallel to (100). Unlike (Ia), the crystal of (IIa) contains centrosymmetric cyclic hydrogen-bonded dimers [graph set R22(14)], formed through strong O-H⋯O hydrogen bonds and are further linked by weak C-H⋯O hydrogen bonds into ribbons extending across [101].

ChemInform Abstract: Conformational Preferences of 2‐Acylpyrroles in Light of FT‐IR and DFT Studies

AbstractReview: 129 refs.

Theoretical Study of Chiral Carboxylic Acids. Structural and Energetic Aspects of Crystalline and Liquid States

Lattice energy calculations by semiempirical and quantum mechanical methods have been carried out on 17 crystals of phenoxypropionic acids (PPAs), including 5 pairs of racemic and homochiral partners. Racemic crystals always consist of centrosymmetric cyclic hydrogen-bonded dimers, while homochiral crystals invariably include chain (“catemer”) motifs of O–H···O hydrogen bonds, except for one case having a pseudo-2-fold axis dimer with two molecules in the asymmetric unit. Energy differences between homochiral and racemic crystals are small, without a consistent trend of higher stability of either state. Partitioned molecule–molecule energy calculations show that hydrogen bonds compete with diffuse dispersive factors or local electrostatic interactions. Monte Carlo methods with empirical atom–atom potentials were also applied to simulate the structural and energetic equilibrium properties of some racemic and homochiral liquids. The latter are very nearly isoenergetic, apparently irrespective of molecular s...

Syntheses, hydrogen-bonded assembly structures, and spin crossover properties of [FeIII(Him)2(n-MeOhapen)]PF6 (Him = imidazole and n-MeOhapen = N,N′-bis(n-methoxy-2-oxyacetophenylidene)ethylenediamine); n = 4, 5, 6)

Three iron(III) complexes, [FeIII(Him)2(n-MeOhapen)]PF6 (1: n=4, 2: n=5, 3: n=6), where Him=imidazole and n-MeOhapen=N,N′-bis(n-methoxy-2-oxyacetophenylidene)ethylenediamine, were synthesized. Each FeIII ion was coordinated by N4O2 donor atoms of equatorial n-MeOhapen and two axial Him. The saturated FeC2N2 chelate ring involving the ethylenediamine moiety adopted a gauche conformation and the two phenylidene planes of [FeIII(Him)2(n-MeOhapen)]+ were oriented opposite to the FeO2N2 coordination plane. Two adjacent [FeIII(Him)2(4-MeOhapen)]+ cations in 1 were connected via PF6− ions by hydrogen bonds between the imidazole group and PF6− to give a one-dimensional chain. Two adjacent cations in 2 were connected via hydrogen bonds between the phenylidene oxygen and imidazole atoms to form a cyclic dimer structure. Two EtOH molecules were involved in a hydrogen-bonded cyclic dimer structure in 3. Compounds 1 and 2 showed spin crossover behavior, but 3 showed incomplete spin crossover.

Synthesis, structure, and spin equilibrium properties of [FeIIIX2L]BPh4⋅solvents (X = 1-methylimidazole and imidazole; L = N, N′-bis(3-ethoxycarbonylsalicylidene)ethylenediamine)

Two iron(III) complexes [FeIIIX2L]BPh4⋅solvents (X=1-Meim (1), Him (2)) were synthesized and the crystal structures were determined, where H2L=N, N’-bis(3-ethoxycarbonylsalicylidene)ethylenediamine, 1-Meim=1-methylimidazole, Him=imidazole, BPh4−=tetraphenylborate. FeIII ion has an octahedral coordination environment by N2O2 donor atoms of equatorial L2− and N2 donor atoms of axial imidazoles. Complex 1 is described as isolated molecule, while complex 2 has a hydrogen-bonded cyclic dimer structure constructed by hydrogen-bond between imidazole group and ethoxycarbonyl oxygen via ethanol. Complex 1 is in a high-spin (S=5/2) state over the whole temperature region 5–300K, while complex 2 showed a gradual complete spin equilibrium between high and low-spin states at T1/2=192K.

H/D isotopic recognition and temperature effects in IR spectra of hydrogen-bonded cyclic dimers in crystals: 3-Methylcinnamic acid and 4-phenylbutyric acid

In the present work, the experimental and theoretical study of the nature of the inter-hydrogen bond interactions in two different carboxylic acids, 3-methylcinnamic acid (3MCA) and 4-phenylbutyric acid (4PBA), were reported. The polarized IR spectra of 3MCA and 4PBA crystals were recorded at the frequency ranges of the νOH and νOD bands. The spectral properties of 3MCA and 4PBA interpreted with the aid of the calculations based on the “strong-coupling” model. The differences in the spectral properties of the two different dimeric systems in the crystals provide a valuable information about the existence of a direct relationship between the crystal spectral properties in IR and the electronic structure of the molecular systems. In 3MCA crystals strong vibrational exciton interactions favor a “tail-to-head” (TH)-type Davydov coupling widespread via the π-electrons, whereas in 4PBA crystals a weak “through-space” (SS) exciton coupling is responsible for a “side-to-side”-type coupling. The relative contribution of each individual exciton coupling mechanism in IR spectra generation strongly depends on temperature and molecular electronic structure. The H/D isotopic recognition effect, depending on a non-random distribution of protons and deuterons in the crystal hydrogen bridges, was also analyzed.

Conformational Preferences of 2-Acylpyrroles in Light of FT-IR and DFT Studies

Conformations of alpha-substituted pyrroles have been effectively studied using spectroscopic methods assisted by theoretical calculations developed in the recent decade. The question of how to effectively study the conformation of 2-acylpyrrole no longer remains unanswered. The detailed spectroscopic studies conducted in the last decade and interpreted on the basis of theoretical calculations provide a satisfactory answer to that question. Based on the Density Functional Theory (DFT) calculations of conformational properties of 2-acylpyrroles, for which two stable rotameric forms were predicted, syn and anti-conformers have been studied either by experimental or theoretical methods. The family of 2-acylpyrroles have both a proton donor N-H group and a proton acceptor C=O group. This structure favors the formation of doubly hydrogen-bonded cyclic dimers connected by two N-H...O=C bonds. The tendency to form cyclic dimers stabilizes the syn-conformation. Due to these properties 2-acylpyrroles can be used as structural models for the conformational analysis of peptides. This review summarizes recent investigations of conformations of 2-acylpyrroles, with a particular emphasis on the hydrogen bonds forming within these systems. The influence of 2-substitution on different aspects of stability of these molecular systems and the usefulness of infrared spectroscopy supported by theoretical calculations in H-bonds and conformational studies are discussed. Among the molecular properties hydrogen bond energy, structural characteristics such as C=O bond length of dimers and unique spectral features of 2-acylpyrroles that can be used to predict and investigate the conformation and structure of proteins are considered.

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

N-(4,6-Dimethylpyrimidin-2-yl)-1,3-benzothiazol-2-amine

In the title compound, C13H12N4S, an amino N atom is connected to a 1,3-benzothia­zole fused-ring system and a dimethyl-substituted pyrimidine ring, these components being aligned [inter­planar dihedral angle = 1.9 (1)°]. The secondary amino N atom forms an inter­molecular N—H⋯N hydrogen bond to an N atom of the fused ring of an adjacent mol­ecule, generating a centrosymmetric cyclic hydrogen-bonded dimer [graph set R 2 2(8)].

Polarized IR Spectra of the Hydrogen Bond in Two Different Oxindole Polymorphs with Cyclic Dimers in Their Lattices

This article focuses on the problem of remarkably strong changes in the fine structure patterns of the ν(N-H) and ν(N-D) bands attributed to the hydrogen and deuterium bonds accompanying the phase transition, which occurs between two polymorphic forms of oxindole. The lattices of these two different crystals contain hydrogen-bonded cyclic dimers differ in their geometry parameters. The source of these differences in the polymorph spectral properties results from the geometry relations concerning the dimers constituting the lattice structural units. In the case of the "alpha" phase, the hydrogen bond lengths of the dimers differ by 0.18 Å. This leads to the "off-resonance exciton coupling" weakly involving the dimer hydrogen bonds. For the "beta" phase, with practically symmetric dimers in the lattice, the spectra become typical for centrosymmetric hydrogen bond systems due to the full resonance of the proton or deuteron vibrations.

Diisopropyl-ammonium methane-sulfonate.

The title molecular salt, C6H16N+·CH3SO3 −, has been determined at 150 K. Two diisopropyl­ammonium cations (dipH) and two anions form N—H⋯O hydrogen-bonded cyclic dimers lying around centers of symmetry. Only two of the three O atoms of the methane­sulfonate anion are involved in hydrogen bonding, resulting in slightly longer S—O bond lengths. The title structure represents an example of a sulfonate anion that is part of a hydrogen-bonding R 4 4(12) graph-set motif, which is well known for related dipH acetates. Additionally, the Raman and the IR spectroscopic data for the title compound are presented.

1-n-Decyl-5-nitro-1H-benzimidazol-2(3H)-one

The benzimidazolone part of the title mol­ecule, C17H25N3O3, is almost planar (r.m.s. deviation = 0.016 Å) and its mean plane is aligned at 7.9 (4) ° with respect to the mean plane of the nitro substituent. In the crystal, two mol­ecules are disposed about a center of inversion, generating a N—H⋯O hydrogen-bonded cyclic dimer with a R 2 2(8) graph-set motif.

5-Nitro-1-n-octyl-1H-benzimidazol-2(3H)-one

The benzimidazolone part of the mol­ecule of the title compound, C15H21N3O3, is almost planar (r.m.s. deviation = 0.007 Å) with its mean plane aligned at a dihedral angle of 10.4 (3)° with respect to the mean plane of the nitro substituent. In the crystal, two mol­ecules are disposed about a center of inversion, generating an N—H⋯O hydrogen-bonded cyclic dimer with R 2 2(8) graph-set motif.

Gallic acid

Anhydrous 3,4,5-trihy­droxy­benzoic acid, C7H6O5, is essentially planar, with its non-H atoms exhibiting mean and maximum deviations from coplanarity of 0.014 and 0.0377 (5) Å, respectively. The C—C—C—OH torsion angle about the bond linking the carboxyl group to the benzene ring is −0.33 (10)°. In the crystal, the –COOH groups form centrosymmetric hydrogen-bonded cyclic dimers [graph set R 2 2(8)] and the phenolic –OH groups participate in both intra- and inter­molecular hydrogen bonds, forming a three-dimensional network structure.

Excited-State Double Proton Transfer Dynamics of Model DNA Base Pairs: 7-Hydroxyquinoline Dimers

The excited-state double proton transfer of model DNA base pairs, 7-hydroxyquinoline dimers, in benzene has been investigated using picosecond time-resolved fluorescence spectroscopy. Upon excitation, whereas singly hydrogen-bonded noncyclic dimers do not go through tautomerization within the relaxation time of 1400 ps, doubly hydrogen-bonded cyclic dimers undergo excited-state double proton transfer on the time scale of 25 ps to form tautomeric dimers, which subsequently undergo a conformational change in 180 ps to produce singly hydrogen-bonded tautomers. The rate constant of the double proton transfer reaction is temperature-independent, showing a large kinetic isotope effect of 5.2, suggesting that the rate is governed mostly by tunneling.

Synthesis and Structural Characterization of Diisopropylammonium Trifluoroacetate and Diisoproplyammonium Pentafluoropropionate

Diisopropylammonium trifluoroacetate ({[iPr2NH2][CF3COO]}; dip tfa; 1) and diisopropylammonium pentafluoropropionate ({[iPr2NH2][C2F5COO]}; dip pfp; 2) have been synthesized and structurally characterized by X-ray diffraction and spectroscopic methods. Both compounds form hydrogen-bonded cyclic dimers (Etter symbol: R4 4 (12)) in the solid state. The asymmetric unit of 1 contains one trifluoroacetate anion and one dip cation in the centrosymmetric space group Pī. The asymmetric unit of 2 consists of two crystallographically independent pentafluoropropionate anions and two independent dip cations forming dimers in the form of rings, both lying around centers of symmetry in the space group Pī. In dip tfa and dip pfp the cations act as double hydrogen bond donors, and each of the two oxygen atoms of the carboxyl group are single hydrogen bond acceptors. The donor acceptor distances of the N-H...O hydrogen bonds are within the expected range for medium strong hydrogen bonds. The quasi-molecular cyclic dimers are connected with neighboring units only by van der Waals interactions.

A study into the effect of subtle structural details and disorder on the terahertz spectrum of crystalline benzoic acid

The phonon modes of crystalline benzoic acid have been investigated using terahertz time-domain spectroscopy, rigid molecule atom-atom model potential and plane-wave density functional theory lattice dynamics calculations. The simulation results show good agreement with the measured terahertz spectra and an assignment of the terahertz absorption features of benzoic acid is made with the help of both computational methods. Focussing on the strongest interactions in the crystal, we describe each vibration in terms of distortions of the benzoic acid hydrogen bonded dimers that are present in the crystal structure. The terahertz spectrum is also shown to be highly sensitive to the location of the carboxylic acid hydrogen atoms in the cyclic hydrogen-bonded dimers and we have systematically explored the influence of the observed disorder in the hydrogen atom positions on the lattice dynamics.

Self-assembled structures formed by a wedge-shaped molecule in 2D and 3D: the role of flexible side chains and polar head groups

A wedge-shaped amphiphilic molecule, 3,4,5-tridodecyloxycinnamic acid, was used as a model system to explore the role of different constitutive elements of the chemical structure in the formation of 2D and 3D self-assemblies. The polar heads forming cyclic hydrogen-bonded dimers determine the two largest unit cell parameters, which depend only slightly on the dimensionality of the system (i.e. 2D versus 3D) and on the sample thermal history. By contrast, the structure of the alkyl side chains is very sensitive to the phase transformations, and is likely to be responsible for the rich polymorphic behaviour of the studied compound. Thus, in the monotropic SmC phase, the alkyl chains form a liquid-crystalline sub-lattice with hexagonal symmetry that can further crystallize either in a triclinic sub-cell (metastable crystalline phase) or in an orthorhombic sub-cell (stable crystalline phase). In 2D, at the interface with the graphite surface the molecular orientation is guided by the epitaxy. Although the largest lattice parameters are close to those in the bulk, the alkyl chains adopt a particular alternating orientation. In one molecule of the dimer, two alkyl chains have their molecular planes parallel to the substrate while the third chain is perpendicular to it, and the other way around for the other molecule of the dimer. To our knowledge, such alternating orientation of the alkyl chains in the monolayer is reported for the first time.