Intermolecular OH Research Articles

Halogen substituted quinolylsalicylaldimines: Four halogens three structural types

A series of halogen substituted 5-X-N-(8-quinolyl)salicylaldimines (HqsalX, X=F 1, Cl 2, Br 3 and I 4) have been prepared, characterized and the crystal structures of all four are reported. The compounds form stacks, in most cases held together either by π–π or lone pair(N)–π interactions. All compounds exhibit an intramolecular OH⋯N hydrogen bond with 2 also displaying an intermolecular OH⋯O hydrogen bonding square. Additional CH⋯N/O and CH⋯π interactions serve to link neighbouring HqsalX molecules with 3 and 4 forming narcissistic dimers. While the halogen has a profound effect on the structure it is not involved in either hydrogen or halogen bonding in any of the structures. DFT calculations suggest that the conformational preference is dependent on the halogen.

TEFDDOLs (α,α,α′,α′-Tetrakis(perfluoroaryl/alkyl)-2,2′-dimethyl-1,3-dioxolane-4,5-dimethanols): Highly Fluorinated Chiral H-Bond Donors and Brønsted Acids with Distinct H-Bonding Patterns and Supramolecular Architectures

The synthesis of six enantiopure α,α,α',α'-tetrakis(perfluoroalkyl/aryl)-2,2'-dimethyl-1,3-dioxolane-4,5-dimethanols (TEFDDOLs), by addition of perfluorinated organolithium reagents or Ruppert's reagent (TMS-CF(3)) to isopropylidene tartaric dichloride, is reported. X-ray crystal structures of the TEFDDOLs alone or in complexes with H-bond acceptors such as water and DABCO revealed that this new class of highly fluorinated chiral 1,4-diols forms distinct intra- and intermolecular H-bond patterns. Intramolecular OH-OH bonding accounts for the relatively high acidity of the perfluoroalkyl TEFDDOLs (pK(a) in DMSO: tetrakis-CF(3), 5.7; tetrakis-C(2)F(5), 2.4). For the tetrakis(perfluorophenyl) TEFDDOL, a quite unusual "pseudo-anti" conformation of the diol, with no intramolecular (and no intermolecular) OH-OH bonds, was found both in the crystal and in solution (DOSY and NOESY NMR). The latter conformation results from a total of four intramolecular OH-F(aryl) hydrogen bonds overriding OH-OH bonding. Due to their H-bonding properties, the TEFDDOLs are promising new building blocks for supramolecular and potentially catalytic applications.

Molecular structure of 4-hidroxy-3-(3-methyl-2-butenyl) acetophenone, a plant antifungal, by X-ray diffraction, DFT calculation, and NMR and FTIR spectroscopy

The molecular structure of two mixed and closely related conformers of the title compound, C13H16O2, found in the solid with unequal occupancies has been determined by X-ray diffraction methods. The substance crystallizes in the monoclinic Pca21 space group with a=17.279(2), b=5.1716(7), c=12.549(2)Å, and Z=4 molecules per unit cell. The structure was solved from 1314 reflections with I>2σ(I) and refined to an agreement R1-factor of 0.049. The minor conformer (34.7%) is nearly mirror-related to and extensively overlapped with the major one. The skeleton of the 4-hydroxyacetophenone molecular fragment and the prenyl group, (CH2)(CH)C(CH3)2, pendant arm attached to it are both planar and perpendicular to each other. A strong intermolecular OH⋯O bond links neighboring molecules in the lattice to produce a polymeric structure. The conformational structures of the compound in the gas phase have been calculated by the DFT method and the geometrical results have been compared with the X-ray data. These data allow a complete assignment of vibration modes in the solid state FTIR and Raman spectra. The calculated 1H and 13C chemicals shifts are in good agreement with the corresponding experimental NMR spectra of the compound in solution.

On the anomalous vibration spectra and O[sbnd]H⋯N bond dictated structure of 3-fluoroisonicotinic acid

The vibrational structure of solid 3-fluoroisonicotinic acid, as measured by IR absorption and Raman spectra in the 4000–50cm−1 region and aided by B3LYP/6-311++G(d,p) and NBO calculations has been analyzed. While anomalous spectral behavior similar to that in pyridine-carboxylic acids has been observed as two broad medium absorptions 2436 and 1870cm−1, the inverted bands observed in isonicotinic acid, are present as ‘normal’ bands near 1488, 1308, 1132, 1062, and 823cm−1. It has been shown by dimer modeling that the absorptions at 2436 and 1308cm−1 correspond to OH stretching and in-plane vibrations originating from inter-molecular OH⋯N bonding. Formation of a network of dimer chains has been shown to be a result of CH⋯O bond links, giving rise to a local center of inversion between monomer species in the network. This has been validated by observing one broad low intensity Raman band at 1708cm−1 and one strong broad IR band at 1727cm−1 assigned as symmetric and anti-symmetric carbonyl modes respectively. In the proposed dimer model, the OH⋯N bond length is calculated to be 2.742Å, shorter than the van der Waals approach, 2.750Å, placing it in the category of a strong hydrogen bond. The CH⋯O bond length for the dimer is calculated to be ∼3.282Å. It has been found that the dimer model is only suggestive of the complex nature of OH⋯N bonding but the results generally are in agreement with experiment.

Tris(hydroxymethyl) aminomethane salt of ramipril: Synthesis, structural characterization from X-ray powder diffraction and stability studies

Tris(hydroxymethyl) aminomethane (tris) salt of API ramipril was synthesized, and characterized by FTIR, TG-DSC and ab initio X-ray powder structure analysis. The compound, ramipril-tris (II), crystallizes in the monoclinic space group P2(1) with a=24.3341(15), b=6.4645(5), c=9.5357(7) Å, β=96.917(3)° and V=1489.1(3) Å(3). The crystal structure has been determined from laboratory X-ray powder diffraction data using direct space global optimization strategy (simulated annealing) followed by the Rietveld refinement. A network of intermolecular OH…O, CH…N and CH…O hydrogen bonds between the ramipril-ramipril, tris-tris and ramipril-tris components in the compound generates a two-dimensional molecular assembly in (110) plane. A comparative study of solid-state stabilities of ramipril-tris (II) with that of ramipril (I) and ramipril-erbumine (III) indicates that ramipril-tris (II) is the most stable one among the three, and the conversion to impurity D after 72 h at 80 °C is only 1.5%. The solution phase analysis at different pH values also reveals a greater stability of ramipril-tris (II) over ramipril (I).

Synthesis and properties of catechol-fused tetrathiafulvalene derivatives and their hydrogen-bonded conductive charge-transfer salts

Catechol-fused tetrathiafulvalene (TTF) derivatives have been designed and synthesized as a new type of π-electron donor molecules having two phenolic hydroxyl groups. Cyclic voltammetry measurements and quantum chemical calculations demonstrated the electronic effect of the direct fusion of the catechol unit to the TTF π-skeleton. In the charge-transfer (CT) salts with bromide or chloride anions, a one-dimensional hydrogen-bonded chain was formed by the intermolecular OH⋯X network between the catechol moieties and the halide anions. The slight dissimilarity of the hydrogen-bond distances for the two CT salts gave rise to the significant differences in their overall molecular arrangements and intermolecular interactions as well as the electrical resistivities.

Experimental and theoretical DFT studies of structure, spectroscopic and fluorescence properties of a new imine oxime derivative

A new imine oxime, (1E,2E)-phenyl-[(1-phenylethyl)imino]-ethanal oxime (I), is synthesized and characterized. The title compound crystallizes in the monoclinic space group P21/c with a=12.3416(7), b=9.5990(6), c=11.9750(7), β=92.417(4) and Z=4. Crystallographic, vibrational (IR), and NMR (1H and 13C chemical shifts) data are compared with the results of density functional theory (DFT) method at the B3LYP/6-311++G(d,p) level. The structure of I is stabilized by intermolecular OH⋯N hydrogen bonds. The theoretical calculations show that the compound exhibits a number of isomers, and the molecular geometry of the most stable optimized isomer (s-trans-E,E) can well reproduce the X-ray structure. The calculated vibrational bands and NMR chemical shifts are consistent with the experimental results. The NBO/NPA atomic charges are performed to explore the possible coordination modes of the compound. The electronic (UV–vis) and photoluminescence spectra calculated using the TD-DFT method are correlated to the experimental spectra. The DMSO solutions of I are fluorescent at room temperature. The assignment and analysis of the frontier HOMO and LUMO orbitals indicates that both absorption and emission bands are originated mainly from the π–π* transitions.

Quantifying intermolecular interaction of anthrylidene methyl arjunolate: Insights from Hirshfeld surface analysis

An anthrilidine derivative of arjunolic acid, namely, anthrylidene methyl arjunolate (1) have been synthesized and characterized by X-ray structural studies with a detailed analysis of Hirshfeld surfaces and fingerprint plots facilitating a comparison of intermolecular interactions in building self-assembled framework. The central six member fused ring, which is flattened due to the presence of a CC double bond, adopts a sofa conformation, whereas other fused six member rings assumes chair conformations. All the fused rings have trans fusion except one ring junction, which is in cis fusion. The crystal packing of (1) exhibits intermolecular OH⋯O and CH⋯O hydrogen bonds forming R33(7) ring motif and are further linked through CH⋯π (arene) bonds to generate a framework. The fingerprint plots enabled to decode intermolecular interaction types present in the title crystal structure and the structures retrieved from the Cambridge Structural Database (CSD). A comparison of Hirshfeld surface in the title compound with similar structure retrieved from the CSD has been presented.

Molecular structure (monomeric and dimeric structure) and HOMO–LUMO analysis of 2-aminonicotinic acid: A comparison of calculated spectroscopic properties with FT-IR and UV–vis

The experimental (UV–vis and FT-IR) and theoretical study of 2-aminonicotinic acid (C6H6N2O2) was presented in this work. The ultraviolet absorption spectrum of title molecule that dissolved in ethanol and water were examined in the range of 200–400nm. The FT-IR spectrum of the title molecule in the solid state were recorded in the region of 400–4000cm−1. The geometrical parameters and energies of 2-aminonicotinic acid have been obtained for all four conformers/isomers (C1, C2, C3, C4) from DFT (B3LYP) with 6-311++G(d,p) basis set calculations. C1 form has been identified the most stable conformer due to computational results. Therefore, spectroscopic properties have been searched for the most stable form of the molecule. The vibrational frequencies were calculated and scaled values were compared with experimental FT-IR spectrum. The complete assignments were performed based on the total energy distribution (TED) of the vibrational modes, calculated with scaled quantum mechanics (SQM) method. Also the molecular structures, vibrational frequencies, infrared intensities were calculated for a pair of molecules linked by the intermolecular OH⋯O hydrogen bond. Moreover, the thermodynamic properties of the studied compound at different temperatures were calculated. Besides, charge transfer occurring in the molecule between HOMO and LUMO energies, frontier energy gap, molecular electrostatic potential (MEP) were calculated and presented. The spectroscopic and theoretical results are compared to the corresponding properties for monomer and dimer of C1 conformer. The optimized bond lengths, bond angles, calculated frequencies and electronic transitions showed the agreement with the experimental results.

Intramolecular and intermolecular OH …O and OH …F interactions in perfluoropolyethers with polar end groups: IR spectroscopy and first-principles calculations

Perfluoropolyether (PFPE) fluids constitute a class of polymers that fulfil a wide range of requirements for hi-tech applications, due to their pefluorinated backbone. For some of these applications they are requested to bear polar end groups, and the combination of a chemical inert backbone and a reactive end group can produce peculiar conformations and supramolecular structures. The molecular structure and the vibrational properties of the ethoxyl-terminated PFPE FLUOROLINK®E10H in solution are here investigated by means of IR spectroscopy. It is shown that the complex spectral features of the OH-stretching region cannot be explained without a thorough computational study, involving the investigation of the conformational space of an isolated model molecule by means of semiempirical AM1 calculations and DFT calculations. The most relevant conformers were singled out, showing a high degree of conformational disorder for FLUOROLINK®E10H. Furthermore, it is shown that intra- and intermolecular H-bonding affects significantly the molecular structure and the vibrational spectrum. Several interactions are shown to be relevant, such as OH …F interactions and complexes with residual water. Theoretical values of the absolute intensities of OH stretching IR bands, relevant for the analytical applications, are obtained.

Systematic Study of Aggregation Structure and Thermal Behavior of a Series of Unique H-Shape Alkane Molecules

The H-shape alkanes of various arm lengths have been synthesized successfully through the Grignard reaction. The detailed investigation of these novel compounds may allow us to widen the topological chemistry field furthermore. The molecular form and molecular packing structure in the crystal lattice have been revealed successfully on the basis of X-ray structure analysis as well as the analysis of Raman longitudinal acoustic modes (LAM) sensitive to the alkyl zigzag chain segments. The molecular conformation in the crystal lattice is deformed markedly from the originally imagined H-shape. In the cases of C3HOH to C6HOH, for example, the molecules are packed in a complicated manner and the OH···O hydrogen bonds govern the whole intermolecular interactions mainly. Since the alkyl segmental length is not very long, the conformational change is not very drastic, i.e., the small configurational entropy. Synergic effect of the hydrogen bonds and the small configurational entropy gives the higher melting point as known from the thermal data. On the other hand, in the cases of C10HOH and C12HOH, one of the long alkyl chain arms is found to be bent by 90° so that all of the alky chain segments of planar-zigzag conformation can be packed as closely as possible, and the intermolecular OH···O hydrogen bonds are also formed effectively without any mistake. As a result, the contribution of nonbonded intra- and intermolecular van der Waals interactions between the trans-zigzag alkyl chain segments become major, and the coupling of this enthalpy effect with the larger configurational entropy effect of the molecular shape results in the decrement of the melting point which approaches gradually that of longer n-alkane compound. In this way a sensitive balance between the nonbonded van der Waals interactions, the OH···O hydrogen bonds, as well as the configurational entropy effect gives the characteristic thermal behavior of the H-shape compounds. The thus-newly synthesized H-shape alkane compounds should give us new insight into the packing topology of complicated molecules, leading to the development of new functionality unexpected for normal linear alkane compounds.

Combined DFT with NBO and QTAIM studies on the hydrogen bonds in (CH3OH) n (n = 2–8) clusters

The (CH3OH)n (n = 2–8) clusters formed via hydrogen bond (H-bonds) interactions have been studied systemically by density functional theory (DFT). The relevant geometries, energies, and IR characteristics of the intermolecular OH···O H-bonds have been investigated. The quantum theory of atoms in molecule (QTAIM) and natural bond orbital (NBO) analysis have also been applied to understand the nature of the hydrogen bonding interactions in clusters. The results show that both the strength of H-bonds and the deformation are important factors for the stability of (CH3OH)n clusters. The weakest H-bond was found in the dimer. The strengths of H-bonds in clusters increase from n = 2 to 8, moreover, the strengths of H-bonds in (CH3OH)n (n = 4–8) clusters are remarkably stronger than those in (CH3OH)n (n = 2, 3) clusters. The small differences of the strengths of H-bonds among (CH3OH)n (n = 6–8) clusters indicate that a partial covalent character is attributed to the H-bonds in these clusters. The linear relationships between the electron density of BCP (ρb) and the H···O bond length of H-bonds as well as the second-perturbation energies E(2) have also been investigated and used to study the nature of H-bonds, respectively.

Crystal conformations and molecular packing of (S)-2-methoxy-2-(9-phenanthryl)propanoic acid and a diastereomeric amide prepared from (R)-2-methoxy-2-(1-naphthyl)propanoic acid

This paper reports the first evidence of the contribution of T-shaped aromatic CH⋯π interactions to the crystallization of 2-aryl-2-methoxypropanoic acid and amide. The crystal structures of (S)-2-methoxy-2-(9-phenanthryl)propanoic acid [(S)-M9PP acid, (S)-3] and a diastereomeric amide 6, prepared from (R)-2-methoxy-2-(1-naphthyl)propanoic acid [(R)-MαNP acid, (R)-1] and (S)-1-(1-naphthyl)ethylamine [(S)-4], were determined by X-ray crystallography. Like those of M9PP and MαNP esters, the carbonyl and methoxy groups of (S)-3 exhibited syn conformation. The crystal structure of (S)-3 was stabilized by consecutive intermolecular OH⋯O hydrogen bonds between the carboxy groups. In addition, the 9-phenanthryl groups formed a herringbone structure via aromatic CH⋯ π interactions. The anti conformation of the carbonyl and methoxy groups was observed in the crystal of amide 6, indicating an NH⋯O hydrogen bond. The two 1-naphthyl groups were parallel to one another and located on the same side of the MαNP plane, forming a herringbone structure with adjacent molecules. NMR analyses suggest that, in solution, intramolecular aromatic CH⋯π interactions induce the 1-naphthyl groups to form a slant-parallel conformation. Namely, both the length and interactions between the substituents are important for crystallization. Normal-phase HPLC separation of diastereomeric amides is also discussed.

Solid-state assembly of oxyfunctionalized calix[4]arene derivatives

The solid-state assembly of four calix[4]arene derivatives bearing one or two rings oxyfunctionalized with epoxy and hydroxyl functional groups has been structurally studied by X-ray crystallography. In three cases the presence of OH groups pointing towards the exterior of the molecule allows the formation of intermolecular OH⋯epoxy H-bonds, which give rise to columnar structures, with zigzag or parallel oriented molecules, or helical arrangement of quadruplex elements. In one instance, in the absence of intermolecular H-bonds, columnar stacks of molecules are obtained mainly through intermolecular van der Waals interactions.

Near-Infrared Analysis of Hydrogen-Bonding in Glass- and Rubber-State Amorphous Saccharide Solids

Near-infrared (NIR) spectroscopic analysis of noncrystalline polyols and saccharides (e.g., glycerol, sorbitol, maltitol, glucose, sucrose, maltose) was performed at different temperatures (30-80 degrees C) to elucidate the effect of glass transition on molecular interaction. Transmission NIR spectra (4,000-12,000 cm(-1)) of the liquids and cooled-melt amorphous solids showed broad absorption bands that indicate random configuration of molecules. Heating of the samples decreased an intermolecular hydrogen-bonding OH vibration band intensity (6,200-6,500 cm(-1)) with a concomitant increase in a free and intramolecular hydrogen-bonding OH group band (6,600-7,100 cm(-1)). Large reduction of the intermolecular hydrogen-bonding band intensity at temperatures above the glass transition (T(g)) of the individual solids should explain the higher molecular mobility and lower viscosity in the rubber state. Mixing of the polyols with a high T(g) saccharide (maltose) or an inorganic salt (sodium tetraborate) shifted both the glass transition and the inflection point of the hydrogen-bonding band intensity to higher temperatures. The implications of these results for pharmaceutical formulation design and process monitoring (PAT) are discussed.

Hydrogen bonding interaction of CpCo(Dithiolene) complex with monocyclic 2-pyridonyl substituent and unexpected formation of dithiolene-fused tricyclic pyridone derivative

One-pot reaction of [CpCo(CO) 2], elemental sulfur with some heterocycle-substituted alkynes (R–C C–HET) produced [CpCo(dithiolene)] complexes with 2PyOBn ( 2), with both 2PyOBn and 2-hydroxy-2-propyl groups (C(OH)Me 2) ( 5), both 2Py and C(OH)Me 2 ( 8), both 4Py and C(OH)Me 2 ( 11), and with 4Py substituent ( 13). A deprotection of benzyl group (Bn) from 2 with trimethylsilyl iodide formed [CpCo(dithiolene)] with 2-pyridonyl substituent ( 3). Heating reaction of 8 without any base resulted in the C(OH)Me 2 group elimination to form the 2-pyridylethylenedithiolate complex ( 9), but 11 underwent only dehydration at the C(OH)Me 2 under heating. While the preparation of 5, the benzyl free complex ( 6) was obtained as a main product. 6 has a dithiolene-fused tricyclic pyridone skeleton. The structures of 3, 5, 6, 8, and 11 were determined by X-ray diffraction studies. Intramolecular OH⋯N( 2Py) hydrogen bondings are found in 5 and 8, and an intermolecular OH⋯N( 4Py) one is found in 11 at solid state. In the 2-pyridonyl complex 3, intermolecular NH⋯O and CH(dithiolene)⋯O hydrogen bondings are observed. 8 showed an intermolecular Cp⋯Cp face-to-face interaction. The tricyclic complex 6 exhibited lower energy electronic absorption ( λ max = 668 nm) compared with the others ( λ max = 562–614 nm), due to an extended π-conjugation of aromatic cobaltadithiolene ring.

Conformational analysis of 2-methyl-1,3,2-dioxaborinane in the presence of a water molecule

By means of nonempirical quantum-chemical approximations RHF//STO-3G, 3-21G, and 6-31G(d) conformational characteristics were studied of molecular associate of 2-methyl-1,3,2-dioxaborinane with water (1:1). A possibility of formation of two-types of complexes was demonstrated: with a donor-acceptor bond O→B and with an intermolecular hydrogen bond OH…O. The calculated parameters of their relative stability and conformational behavior depend both on the reciprocal orientation of the molecules under investigation and on the concepts of the approximation used for the calculation.

1-Methyl-4-[2-(3-methoxy-4-hydroxyphenyl)ethenyl)]pyridinium] hydrogensquarate monohydrate: synthesis, structural investigations and optical properties

1-methyl-4-[2-(3-methoxy-4-hydroxyphenyl)ethenyl)]pyridinium] hydrogensquarate monohydrate (1) has been synthesized and its structure obtained by single crystal X-ray diffraction. Optical properties have been elucidated by means of linear-polarized solid state IR-spectroscopy, UV-spectroscopy as well as nuclear magnetic resonance and thermal analysis. The polarization tool of oriented colloid suspensions in nematic host is used. Quantum chemical calculations have performed with a view to obtaining the electronic structure and optical properties of the novel compound. The compound crystallizes in the space group P-1 and the structure consists of infinite layers, resulting from intermolecular OH…O=C(Sq) (2.684 A) and (Sq)OH…OH2 (2.575 and 2.850 A) hydrogen bonds between the cation and anions as well as solvent molecules.

Hydrogen bonds in dimers of 3-hydroxy-2-methyl-4-pyrone. AIM analysis

According to quantum topological analysis performed at the MP2/6-311++G** level the intramolecular hydrogen bond OH⋯O=C in 3-hydroxy-2-methyl-4-pyrone (maltol) is weak and has ionic nature. This bond is broken upon formation of H-complex of maltol with phosgene and with increase the polarity of medium. The chain dimer of maltol is stabilized by weak intermolecular bonds OH⋯O=C and CH⋯O=C of ionic character, whereas the cyclic dimer by two medium in strength intermolecular hydrogen bonds OH⋯O=C.

N-methylcodeinium iodide—Crystal structure and spectroscopic elucidation

The correlation between the structure and the spectroscopic properties of N-methylcodeinium iodide ( 1) has been studied, using the methods of single crystal X-ray diffraction, IR-LD spectroscopy of oriented samples as a suspension in nematic liquid crystals, UV–vis spectroscopy and 1H and 13C NMR spectroscopy. HPLC tandem mass spectrometry (HPLC ESI MS/MS) and thermal methods were also employed. Quantum chemical calculations have been performed with a view to obtaining the electronic structure and vibrational properties of the title compound. Compound ( 1) crystallizes in the space group P2 12 12 1 and its cations and anions are joined by moderate intermolecular OH…I − interaction of length 3.442 Å. The codeine molecule exhibits the classical T-shape for opiates. A dihedral angle value of 86.4(5)° between the A/B/C and D/E planes is obtained. Rings A and B are effectively coplanar with an interplanar angle of 3.6(3)°.