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Clathrate and Inclusion Compounds. Part 13 [1]. Vibrational and NMR Spectroscopic Studies of Carboxylic Acid Guests in Urea
Abstract
Infrared, Raman and solid state13C NMR spectra have been recorded for arange of inclusion compounds of urea containingstraight chain aliphatic carboxylic acids(butyric – decanoic) as guests. Inclusioncompounds are not formed with formic, acetic andpropionic acids. Thiourea does not forminclusion compounds with any of the C1 to C10acids. The vibrational and NMR data support theconclusion that the acids are present ashydrogen bonded dimers in the channels of thehost. The alkyl chain 13C chemical shiftvalues are very different from those of acidguests in the cavities formed in Dianin'scompound. These suggest that the alkyl chainsare present in the all-trans conformation,although weak bands observed in the spectrum ofthe decanoic acid inclusion compound lend somesupport to suggestions based on MM calculationsthat other conformations might be present.
... For carboxylic acids from propionic to octanoic this guestguest interaction is replaced by a host-guest interaction with the carboxylic acid group interacting with the hydrogen bonded OH groups of the host forming the base of the cavity (Fig. 6b). When accommodated in the urea host (scheme 4) carboxylic acids always exist as hydrogen bonded dimeric species (Davies and Tabner 1998) as this host forms voids in the shape of long channels rather than the discrete cavities found in the Dianin host. ...
This paper reviews the results obtained from vibrational studies (infrared and Raman) of host-guest compounds. These techniques can give information such as: confirmation of inclusion compound formation; host-guest interactions; the state of aggregation and configuration of the guest molecules; the translational and rotational motions of the guest; the spectra of hosts and guests in unusual configurations.
Urea and thiourea form complexes with trifluoromethanesulfonic acid, its monohydrate, and lithium salt CF3SO3Li. Urea complexes with trifluoromethanesulfonic acid are also formed as a result of hydrolysis in the reaction of N,N'-bis(trimethylsilyl)carbodiimide or cyanamide with trifluoromethanesulfonic acid in water.
The synthesis, crystal structure, and properties of novel ternary inclusion compounds formed by the insertion of protonated bis(quinuclidine) guests into urea–bromide and urea–iodide anionic hosts are reported. (Urea2[quinuclidine2H]+Br−), 1, and (urea2[quinuclidine2H]+I−), 2, are monoclinic, space group C2. The cell parameters for 1 are a = 19.323(8), b = 7.145(3), c = 8.566(4), β = 112.19(3), dcalc = 1.284 and Z = 4, considering 472 reflections; for 2 they are a = 20.51(11), b = 7.34(3), c = 8.17(4), β = 111.81(8), dcalc = 1.369, Z = 4, considering 716 reflections. In the two structures each urea molecule interacts with adjacent urea molecules via N–HO hydrogen bonds forming a ribbon-like arrangement. The ribbons are linked through halide ions by N–HX hydrogen bonds forming layered structures. The distances between the layers are 10.301 Å for 1 and 8.566 Å for 2. The compounds may be described as commensurate species. Conductivity values determined for 1 and 2 at room temperature are 1.19 × 10−5 and 8.66 × 10−7 (Ω cm)−1, and they increase with temperature. Aspects of the thermal stability of the products are discussed.
Urea inclusion compounds with different guest species were studied by 13C CP MAS and 1H MAS NMR spectroscopy. It is possible to arrange the asymmetric guest species in three different ways: head–head, head–tail and tail–tail. 13C CP MAS NMR studies indicate that the preference arrangement is determined by the interaction strength of the end functional groups. 13C relaxation experiments are used to study the dynamic properties of urea inclusion compounds. 13C relaxation studies on urea inclusion compounds with n-alkane or decanoic acid show that the 13C T1 and 13C T1ρ values exhibit the position dependence towards the center of the chain, indicating internal chain mobility. The analysis of variable-temperature 13C T1ρ experiments on urea inclusion compounds with hexadecane and pentadecane, for the first time, suggests that chain fluctuations and lateral motion of n-alkane guests may contribute to the 13C T1ρ relaxation.
Infrared and Raman spectra over the temperature range room temperature to 74K have been recorded for a range of inclusion
compounds of thiourea containing monosubstituted cyclohexanes C6H11X (X =Cl,Br,I,CN,NCO) as guests. The liquid phase of all the cyclohexanes consists of an equilibrium mixture of axial and equatorial conformers,
with the equatorial conformer being the more abundant. At room temperature the chloro, bromo and cyano substituted guests
exist predominantly as the axial conformer, whereas the iodo and isocyanato substituted guests exist as a mixture of both
conformers, but with the axial conformer being the more abundant. The iodocyclohexane inclusion compound was the only one
to display a temperature dependent change in the intensity ratio of the conformer bands. This could be due to a change in
the conformer ratio or to a structural phase change.
Large-scale molecular dynamics simulations have been performed on solid inclusion compounds formed between urea and alkane (dodecane) and alkanoic acid (dodecanoic acid) guest molecules. The incommensurate nature of the guest and host substructures means that simulations of these systems are challenging, and our results call into question some of the simplifying assumptions made in earlier simulations on the urea inclusion compounds. Detailed information is obtained on the structural properties of the carboxylic acid dimers and alkyl chains confined within the nanoscale tunnels of the urea host structure, including the chirality of the guest conformation induced by the chiral nature of the urea tunnels. Diffusion coefficients (at 300 K) of the guest molecules along the tunnel axis were determined to be 0.091 ± 0.031 (dodecane) and 0.0063 ± 0.0013 Å(2) ps(-1) (dodecanoic acid), in good agreement with experimental measurements on alkane/urea systems. Weak ordering is observed between guests in neighboring tunnels, which is compatible with experimental measurements on the alkane/urea systems, although the simulations provide more detailed molecular-level insights into the nature of this supramolecular ordering.
The synthesis, crystal structure and properties of a novel ternary inclusion compound formed by protonated bis(quinuclidine) inserted in a urea-chloride anionic host, urea(5)[quinuclidine(2)H]Cl-+(-) (1), are reported. In the host structure each urea molecule interacts with adjacent urea molecules via N-H...O hydrogen bonds forming a channel arrangement. Each hexagonal channel is linked through halide ions by N-H...Cl hydrogen bonds forming a bichannel-like structure. The channel width of the host (14.32 Angstrom) is one of the largest known for a urea host derivative. The compound may be described as a commensurate species, c(g)/c(h) = 0.98. Conductivity determined for 1 at room temperature is 4.00 x 10(-6) (Omega cm)(-1) and it increases with temperature to 3.33 x 10(-4) (Omega cm)(-1) at 77degreesC. Aspects of the thermal stability of the product are discussed.
The intergrowth of 1,10-decanedicarboxylic acid and urea give infinite hydrogen-bonded chains of the guest included in the hexagonal urea host. A deuterium high-resolution solid-state NMR study of the selectively deuterated intergrowth compound 1,10-decanedicarboxylic acid/hydrogenated urea at variable temperature in the range 90 < or = T < or = 300 K was performed on a single crystal. The analysis of the second moment as a function of temperature is shown to be compatible with the known phase transition occurring near T(c) = 203 K. Moreover, the spectra indicate that the orientational disorder is strong, and is compared to an axial uniform disorder. For this purpose, the general equation for the second moment of a system with uniform two-dimensional axial orientational disorder is given, and a method to take into account the non-uniform excitation of the pulse sequence is proposed.
Information about the structure of urea in a urea complex and the endocytic molecules contained therein may be obtained from infrared absorption spectra. Several complexes of aliphatic compounds, including paraffins, bromides, alcohols, acids, and esters, have been examined in this respect.
Raman spectroscopy is shown to provide a rapid and definitive analysis of the nature of urea inclusion compounds. It is demonstrated that the photodecomposition of included alkanones does not destroy the urea lattice, but the inclusion compounds of n-decane are destroyed by ultra sonic agitation.
For some compounds it is possible to form both a urea and a thiourea adduct (inclusion compound). When the length of channel occupied by a molecule of the compounds is measured with the use of continuous layer lines in the x-ray diffraction pattern of a single crystal of the adduct, the length measured in thiourea is appreciably shorter than that measured in urea. The channel length occupied by a molecule depends mainly upon 1. the number of atoms in the chain, 2. the degree of coiling, 3. the amount of overlapping of the ends and, 4. whether the guest is “locked into” the structural features of the host.Data are given for the channel lengths of a number of compounds, some measured in the urea system, some in the thiourea system and some in both systems. From these data it is possible to compute the amount of coiling, the amount of overlapping of ends and the channel lengths of parts of molecules.
The solid state 13C NMR spectra of a series of aliphatic carboxylic acids as guests in various host lattices are reported. The information is compared with that obtainable from infrared spectroscopy and X-ray crystallography.
The CH dipolar spectra of n‐heptane, n‐octane, n‐nonane, and n‐decane in urea inclusion compounds were separately obtained for the α‐, β‐, and inner‐CH2 and CH3 groups using the SASS (switching‐angle sample spinning) NMR method. The CH dipolar coupling constant for the CH2 group decreases with the increasing distance from the center of the molecule and with the decreasing chain length. MM2 molecular mechanics calculations suggested that the included molecule can have various conformations, and provided their geometries and populations. The experimental results could be reproduced by using the calculated parameters and assuming the occurrence of dynamical disorder of various conformations in addition to rotation of the included molecule around the long axis. This is the first evidence for the existence of conformations other than all‐anti in the included n‐alkane molecule; it has long been taken to be in the all‐anti conformation. Previous studies which were explained by the all‐anti conformation are reinterpreted by dynamical disorder of various conformations.
MM2 molecular mechanics calculations for clathrates of Dianin's compound with n-pentane, n-hexane, n-heptane, n-octane, and n-nonane showed the existence of various conformers for enclathrated n-alkanes. The all-anti conformer of n-pentane as well as that of n-hexane comprises ca. 90% of all the probable conformers in the cavity, but that of n-heptane comprises less than 1%. The all-anti conformers of n-octane or n-nonane cannot exist in the clathrate. The possibility of formation of the clathrates is discussed on the basis of free energies evaluated for the inclusion process, which can reproduce the experimental guest selectivity of the Dianin's compound host for n-alkanes. On the assumption of the occurrence of dynamical conformational disorder for the enclathrated n-alkanes, observed C-13 chemical shift changes of the n-alkanes due to enclathration are well-correlated with those obtained by ab initio calculations using Ditchfield's gauge-invariant atomic orbitals.
13C NMR chemical shifts of n-alkanes (C7H16-C20H42, 7-20) in the urea inclusion compounds were measured by the 13C CPMAS NMR method. The 13C chemical shifts of the methyl and α- and β-methylene carbon atoms for 9-20 are independent of the chain lengths of the n-alkane molecules, whereas those for the γ-methylene carbon atoms move downfield with increasing chain length. The ε- and η-methylene 13C resonance signals of some odd n-alkanes were detected as an isolated line. Additivity parameters for the 13C chemical shifts of 9-20 and characteristic features for those of 7 and 8 are discussed.
The solid-phase behavior of the urea inclusion adducts of 1-eicosanol and eicosanoic acid has been studied by vibrational (infrared and Raman) spectroscopy. The urea adduct of 1-eicosanol undergoes a phase transition centered at 210 K while the transition is centered at 250 K in the case of eicosanoic acid. From the vibrational spectra it is possible to differentiate between the effects of the transition on the urea channel and on the guest molecules. In this manner, it is found that the distortion of the urea channel structure occurs in all cases abruptly in narrow (3-4 K) temperature ranges while the onset of orientational disorder of the included chains occurs typically over wider (20-30 K) temperature ranges. The nature of these transitions is the same as previously found for other urea adducts.
Infrared, Raman and solid state 13C-NMR spectra have been recorded for a range of clathrates of Dianin''s compound containing straight chain aliphatic carboxylic acids (formic - octanoic) as guests. The IR, Raman and NMR spectra can be satisfactorily interpreted in terms of dimer (formic and acetic) and monomer (propionic - octanoic) occupation of the cavities. The clathrates containing straight chain alcohol guests (methanol - octanol) have also been prepared to aid in the interpretation of the NMR data.