Hydrogen-bonded Molecular Chains Research Articles

Hydrogen-bonded one-dimensional molecular chains on ultrathin insulating films: Quinacridone on KCl/Cu(111)

Hydrogen-bonded one-dimensional molecular chains on ultrathin insulating films: Quinacridone on KCl/Cu(111)

Competition of polar and antipolar states hidden behind a variety of polarization switching modes in hydrogen-bonded molecular chains.

Switchable π-electron systems are very powerful fragments to emphasize ferroelectric or antiferroelectric polarizations up to record-high levels among organic molecular crystals. According to the Cambridge Structural Database, many azole crystals such as imidazoles and tetrazoles contain polar and bistable hydrogen-bonded molecular sequences suitable for ferroelectricity or antiferroelectricity. Indeed, polarization hysteresis experiments on the 5-phenyl-1H-tetrazole (PHTZ) family combined with single crystal structural analysis have revealed one ferroelectric, two antiferroelectrics, and two hybrid-like dielectrics. Here, the rich variations for the interrelation between the hydrogen-bonding states and the polarization switching modes are interpreted by density functional theory (DFT) calculations with an excellent consistency. Large switchable polarizations are theoretically confirmed, and, as expected, the largest contribution is the switchable π-electron systems. By mapping the energy levels of polar/antipolar states, the disordered hydrogen bonds always appear when the ground state is accompanied by a nearly degenerate state. The straightforward case is the hybrid-like dielectric caused by the competition between the polar and antipolar states. However, contrastive behaviors are observed when the switchable dipoles are involved in competition between the different antipolar arrangement. For example, the PHTZ crystal exhibits typical antiferroelectric switching regardless of the hydrogen disorder, whereas polarization switching is silent in the imidazole derivatives. The latter is explained by the switching field increase with depth of the ground state relative to the energy level of the polar state.

A novel crystal form of metacetamol: the first example of a hydrated form.

We report the crystal structure and crystallization conditions of a first hydrated form of metacetamol (a hemihydrate), C8H9NO2·0.5H2O. It crystallizes from metacetamol-saturated 1:1 (v/v) water-ethanol solutions in a monoclinic structure (space group P21/n) and contains eight metacetamol and four water molecules per unit cell. The conformations of the molecules are the same as in polymorph II of metacetamol, which ensures the formation of hydrogen-bonded dimers and R22(16) ring motifs in its crystal structure similar to those in polymorph II. Unlike in form II, however, these dimers in the hemihydrate are connected through water molecules into infinite hydrogen-bonded molecular chains. Different chains are linked to each other by metacetamol-water and metacetamol-metacetamol hydrogen bonds, the latter type being also present in polymorph I. The overall noncovalent network of the hemihydrate is well developed and several types of hydrogen bonds are responsible for its formation.

Bifunctional Behavior of a Porphyrin in Hydrogen-Bonded Donor–Acceptor Molecular Chains on a Gold Surface

Peculiar hydrogen-bonded molecular chains are spontaneously created from the self-assembly on a gold surface of a porphyrin functionalized with four aromatic amine moieties. The molecular chains are formed by a sequence of dyads, where the same molecule behaves alternately as a hydrogen-bond acceptor or donor as a whole at all its four aromatic amino groups. This remarkable bifunctional behavior is due to the conformational flexibility of the functionalizing amino groups that switch from a planar, aniline-like conformation in donors to a pyramidal, amine-like one in acceptors. Furthermore, we show that the acceptor porphyrins can trap gold adatoms underneath their center. Combined scanning tunneling microscopy experiments and density functional theory calculations characterize the structural and electronic modifications suffered by such molecules to establish amino–amino interactions. Notably, scanning tunneling spectroscopy measurements show that the highest occupied molecular orbital–lowest unoccupied m...

Temperature- and pressure-induced phase transitions in cyclobutanol

The phase transition and polymorphism of cyclobutanol (C4H8O) has been investigated at low temperature and high pressure. Differential scanning calorimetry (DSC) and Raman spectra reveal that a supercooled state is observed during the cooling process, while crystalline state is formed in the heating process. We also present pressure-induced phase transition of cyclobutanol by means of Raman and infrared spectroscopy. The results indicate that cyclobutanol undergoes two phase transformations during compression to 11.4GPa. At around 0.9GPa, the liquid cyclobutanol transforms to a solid crystal structure. Further compression to 1.4GPa, another fully ordered crystalline phase is observed. Simultaneously, conformational change is observed accompanied by phase transition. In addition, the red shift of the O–H stretching modes with pressure suggests the ordered crystalline phases are characterized by the formation of hydrogen-bonded molecular chains. Finally, the phase transitions under high pressure or low temperature are reversible.

High pressure and low-temperature polymorphism in cyclopentanol

The polymorphism of cyclopentanol (C5H10O) has been investigated as a function of temperature at ambient pressure and as a function of hydrostatic pressures to 3.7 GPa at room temperature. Differential scanning calorimetry (DSC) and Raman spectra reveal that two plastic phases and two fully ordered crystalline phases are formed during cooling. High pressure Raman and infrared spectra show that cyclopentanol undergoes two-phase transformations. At around 0.6 GPa, the liquid cyclopentanol transforms to a solid plastic structure. On further compression to 1.9 GPa, one fully ordered crystalline phase is observed. Based on pieces of evidence such as peak splitting and emergence of new peaks, it can be concluded that the ordered crystalline structure has a lower symmetry. In addition, the decrease in the wavenumber of the O–H stretching modes at low temperature and high pressure suggests the ordered crystalline phases are characterized by the formation of hydrogen-bonded molecular chains.

Temperature dependence of one-dimensional hydrogen bonding in morpholinium hydrogen chloranilate studied by 35Cl nuclear quadrupole resonance and multi-temperature X-ray diffraction

The temperature dependence of (35)Cl NQR frequencies and the spin-lattice relaxation times T(1) has been measured in the wide temperature range of 4.2-420 K for morpholinium hydrogen chloranilate in which a one-dimensional O-HO hydrogen-bonded molecular chain of hydrogen chloranilate ions is formed. An anomalous temperature dependence of the NQR frequencies was analyzed to deduce a drastic temperature variation of the electronic state of the hydrogen-bonded molecular chain. The hydrogen atom distribution in the OHO hydrogen bond is discussed from the results of NQR as well as multi-temperature X-ray diffraction. Above ca. 330 K, the T(1) showed a steep decrease with an activation energy of ca. 70 kJ mol(-1) and with an isotope ratio (37)Cl T(1)/(35)Cl T(1) = 0.97 ± 0.2. The orientational change of the z axis of electric field gradient tensor in conjunction with the hydrogen transfer between adjacent hydrogen chloranilate ions is suggested as a possible relaxation mechanism.

Spontaneous self-assembly of aromatic cyclic dipeptide into fibre bundles with high thermal stability and propensity for gelation

Cyclic dipeptides (CDPs) are the simplest members of cyclic peptides exhibiting exceptional rigidity and stability. A detailed study on the spontaneous self-assembly of aromatic CDP (Phe-Phe) into fibre bundles with 1–2 μm thick and several millimetres long is described. These fibre bundles exhibit the structural hierarchy that is found in natural fibres such as spider silk and collagen. The solubility studies in various solvents provided more insights into the existence and nature of fibre bundles. Fibre bundles transform to gel in chloroform at critical concentration of added trifluoroacetic acid. Thermogravimetric analysis data indicated high thermal stability with multiple transitions attributed to the existence of structural hierarchy in fibre bundles. NMR studies revealed that aromatic π–π interactions along with intermolecular (N–H…O) hydrogen-bonded molecular chains are mainly responsible for the formation as well as observed high stability of fibre bundles. This detailed study of structural hierarchy, solubility, gelation and thermal stability demonstrates the robustness of aromatic CDP (Phe-Phe) to form fibre bundles.

Nature of the vibron self-trapped states in hydrogen-bonded macromolecular chains

We study the influence of temperature and the values of basic energy parameters on the character of vibron self-trapped states in quasi-one-dimensional hydrogen-bonded molecular chains. Investigations have been carried out within the one-dimensional Holstein molecular crystal model employing the variational extension of the Lang-Firsov unitary transformation. It was found that, in the low-temperature regime, only partially dressed small-polaron states may exist. With the rise of temperature, the system enters the metastability region, where partially dressed (light and mobile) and fully dressed (heavy and practically immobile) small-polaron states may exist simultaneously.

Structure of Methyl N-(4-methoxyphenylmethyl)-N′-cyano-carbamimidothioate and Methyl N-[1-(phenylmethyl)-4-piperidinyl]-N′-cyanocarbamimidothioate

The title compounds, Methyl N-(4-methoxyphenylmethyl)-N′-cyanocarbamimidothioate, I, and Methyl N-[1-(phenylmethyl)-4-piperidinyl]-N′-cyanocarbamimidothioate, II, have been designed and synthesized for use as new potential organic molecular electronic materials. The crystal structure of I and II were determined with crystal data (I: Monoclinic, P21/c, a = 4.746(2) A, b = 5.737(3) A, c = 17.399(7) A, β = 91.667(7)o, R all = 0.0703; II: Orthorhombic, Pna21, a = 18.209(8) A, b = 11.463(5) A, c = 7.539(3) A, β = 90.00 o, R all = 0.0481). N–H···N hydrogen bonds were responsible for the formation of one-dimensional zigzag molecular chains of I, and trifurcated hydrogen-bonded molecular chains were indicated in structure of II. C–H···π and C–H···N hydrogen bonds were found in both structures. All these types of interaction together form an extended three-dimensional network and stabilize the title crystals. Two N′-cyanocarbamimidothioates, which were designed and synthesized for use as a new potential organic molecular electronic materials, have been characterized by X-ray diffraction.

Spontaneous self-assembly of designed cyclic dipeptide (Phg-Phg) into two-dimensional nano- and mesosheets

In this study, we present the spontaneous self-assembly of designed simplest aromatic cyclic dipeptides of (l-Phg-l-Phg) and (d-Phg-l-Phg) to form highly stable two-dimensional (2D) nano- and mesosheets with large lateral surface area. Various microscopy data revealed that the morphology of 2D mesosheets resembles the hierarchical natural materials with layered structure. Solution and solid-state NMR studies on cyclo(l-Phg-l-Phg) revealed the presence of strong (N–H–O) hydrogen-bonded molecular chains supported by aromatic π–π interactions to form 2D mesosheets. Interestingly, cyclo(d-Phg-l-Phg) self-assembles to form single-crystalline as well as non-crystalline 2D rhomboid sheets with large lateral dimension. X-ray diffraction analysis revealed the stacking of (N–H–O) hydrogen-bonded molecular layers along c-axis supported by aromatic π–π interactions. The thermogravimetric analysis shows two transitions with overall high thermal stability attributed to layered hierarchy found in 2D mesosheets.

Many-body interactions and the electric response of hydrogen-bonded molecular chains

Quantitative analysis of the impact of intermolecular interactions on the nonlinear electric response of hydrogen-bonded molecular chains has been performed. In particular, the theoretical description of cooperative effects (nonadditivity) based on the many-body calculations is provided. Nonlinear optical response of H-bonded chains (linear and zigzag HF⋯(HF) n , linear H 2CO⋯(H 2CO) n and H 3N⋯(HF) n , where n = 1–4) has also been studied. Values of the static electric dipole moment, polarizability and first-order hyperpolarizability have been calculated and analyzed at the MP2 level of theory using Dunning’s correlation-consistent basis set. The site–site function counterpoise (SSFC) method has been applied in order to avoid basis set superposition error (BSSE). Particularly interesting observations have been drawn in the case of first-order hyperpolarizability.

A New Polymorph of N,N′-Dimethylurea Characterized by X-ray Diffraction and First-Principles Lattice Dynamics Calculations

In this study we present a combined crystallographic and computational study of a new polymorph of N,N'-dimethylurea (DMU) with P2(1)2(1)2 space group symmetry, along with a revised theoretical study of the previously known phase in its corrected space group (Fdd2). X-ray diffraction studies show crystal structures that are very similar, differing only in the relative orientation of the hydrogen-bonded molecular chains that are common to both phases. The vibrational spectra were obtained from B3LYP hybrid functional lattice dynamics calculations and compared with the experimental data for the known phase. The free-energy difference between the forms is derived from the Gamma-point optical mode frequencies, and amounts to less than 1 kJ mol(-1) across the temperature range of interest. The electronic densities-of-states of both phases are also computed, yielding only marginal differences in valence and conduction band compositions and band gap widths. Taken together, the results highlight the small but important differences separating the two crystal lattices.

Polymorphism in cyclohexanol

The crystal structures and phase behaviour of phase II and the metastable phases III' and III of cyclohexanol, C(6)H(11)OH, have been determined using high-resolution neutron powder, synchrotron X-ray powder and single-crystal X-ray diffraction techniques. Cyclohexanol-II is formed by a transition from the plastic phase I cubic structure at 265 K and crystallizes in a tetragonal structure, space group P42(1)c (Z' = 1), in which the molecules are arranged in a hydrogen-bonded tetrameric ring motif. The structures of phases III' and III are monoclinic, space groups P2(1)/c (Z' = 3) and Pc (Z' = 2), respectively, and are characterized by the formation of hydrogen-bonded molecular chains with a threefold-helical and wave-like nature, respectively. Phase III crystallizes at 195 K from a sample of phase I that is supercooled to ca 100 K. Alternatively, phase III may be grown via phase III', the latter transforming from supercooled phase I at ca 200 K. Phase III' is particularly unstable and is metastable with respect to both I and II. Its growth is realised only under very restricted conditions, thus making its characterization especially challenging. The cyclohexanol molecules adopt a chair conformation in all three phases with the hydroxyl groups in an equatorial orientation. No evidence was found indicating hydroxyl groups adopting an axial orientation, contrary to the majority of spectroscopic literature on solid-state cyclohexanol; however, the H atom of the equatorial OH groups is found to adopt both in-plane and out-of-plane orientations.

High-temperature protonic motion and low-temperature lattice deformation in one-dimensional hydrogen-bonded molecular chain in tetramethylpyrazine–chloranilic acid (1:1)

High-temperature protonic motion and low-temperature lattice deformation in one-dimensional hydrogen-bonded molecular chain in tetramethylpyrazine–chloranilic acid (1:1)

Modification of phonon spectra due to vibron self-trapping in molecular crystals

Possible modification of the phonon spectra due to the presence of small-polaron arising on account of vibron (amid-I quanta) self-trapping in hydrogen-bonded molecular chains is discussed. We predict that small-polaron effect should produce characteristic temperature variation of phonon frequencies and small-polaron binding energy. These effects should be observed in the experiments such as measurements of the speed of sound and infrared absorption spectra of molecular crystals which open an interesting possibility for the indirect confirmation of the existence of self-trapped states in molecular chains. Infrared absorption spectra may be especially interesting in that sense since the anticipated temperature variation of binding energy would be observed as a shift of the position of the unconventional (temperature dependent) peak in the IR absorption spectrum towards the position of the normal (temperature independent) one.

High-pressure polymorphism of cyclopentanol (C5H10O): the structure of cyclopentanol phase-V at 1.5 GPa

The fully ordered high-pressure crystal structure of cyclopentanol (C5H10O) has been solved using single-crystal X-ray diffraction techniques on station 9.8 at the SRS Daresbury Laboratory. At pressures above 1.5 GPa, cyclopentanol crystallizes in the monoclinic P2(1)/c space group with a=17.882 (3), b=5.4573 (3), c=9.6817 (14) A, beta=104.699 (8) degrees and Z'=2. The crystal structure is characterized by the formation of hydrogen-bonded molecular chains, denoted C_2;2(4) in graph set notation, which lie parallel to the crystallographic c-axis, with the molecules adopting a pseudo fourfold arrangement around the central core of hydrogen bonds.

Structural Data on Regular Poly(ester amide)s Derived from Even Diols, Glycine, and Terephthalic Acid

The crystalline structure of two sequential poly(ester amide)s derived from glycine, terephthalic acid, and 1,6-hexanediol or 1,12-dodecanediol has been investigated using X-ray and electron diffraction and real space electron microscopy. Crystal packing shows features of both polyamides and polyesters. The structures of the two studied poly(ester amide)s are characterized by the establishment of strong hydrogen-bond interactions along a single direction. The morphology of lamellar crystals has been investigated, their high aspect ratio being consistent with the existence of a preferential crystal growth direction. A deviation from an all-trans conformation has been detected for both polymers. Differences in crystal packing have been found depending on the number of aliphatic methylene groups. In this way, orthorhombic and triclinic unit cells have been deduced for the dodecanediol and the hexanediol derivatives, respectively. Their structures are based on a different arrangement of sheets constituted by hydrogen-bonded molecular chains.

Resonant two-wave interaction in the Davydov model

The Davydov model for exciton–phonon coupling in hydrogen-bonded molecular chains is reconsidered in the context of two-wave resonant interaction. By applying a semi-discrete slowly varying envelope approximation, when the physical problem is that of the long-distance evolution of an input finite duration excitonic pulse, we derive an integrable limit model which preserves the coupling nature of the process. The spectral transform is constructed with emphasis on the complete characterization of the spectral data. As an application, the localized one-soliton solution is explicitly constructed. Then by using Darboux–B¨ acklund transformations, a non-local (or topological) one-soliton solution is also derived. As a consequence, the system possess two different soliton solutions where the phonon component is a localized pulse, but where the exciton wave is either localized (bell shape) or topological (kink shape). The resulting approximate soliton solutions of the Davydov model in the resonant regime are subsonic in the localized case and supersonic in the topological case. Finally, by expressing the Bianchi superposition theorem, a nonlinear superposition formula is derived allowing for explicit two-soliton solution.

Kink solitons in hydrogen-bonded molecular chains

Using the energy analysis method, we study the motion of a kink pair in the presence of an external force and damping, based on a new two-component soliton model. The energy and the effective mass of a kink pair are found. The nucleation rate, the mobility and the conductivity of a kink pair are also calculated. The calculated results are in good agreement with the experimental data.