Hydrogen-bonded Chains Research Articles

Alternate way of soliton solutions in hydrogen-bonded chain

The transport of energy and charge along one-dimensional chains of hydrogen bonds is an extremely important problem in bioenergetic and solid-state situations. We present an alternate way to investigate the proton dynamics in a symmetric double-well potential created by the potentials of two heavy ions in a long periodic chains of hydrogen bonds forming the channels for proton transport. We formulate the Hamiltonian by incorporating quartic anharmonic proton–proton interaction. We invoke the modified extended tangent hyperbolic method (METF) embedded with symbolic computation to solve the associated two coupled equations of motion. We propose a series of new forms of the potential relief of hydrogen bonds. We have shown that the symmetric double-well potential in the presence of anharmonic quartic proton–proton interaction gives rise to the anti-kink, anti-soliton, and soliton solutions for the equations of motion. Thereby the proton motion in the form of coherent energy profiles such as kink and solitons may provide the mechanism of bioenergy transport in biological systems.

Absolute structure of (3aS,5S,7aS,7bS,9aR,10R,12aR,12bS)-7b-hy-droxy-4,4,7a,9a,12a-penta-methyl-10-[(2'R)-6-methyl-heptan-2-yl]-2,8,9-trioxo-octa-deca-hydro-benzo[d]indeno-[4,5-b]azepin-5-yl acetate from 62-year-old crystals.

The structure of the title compound, C32H51NO6, was determined from 62-year-old crystals at room temperature and refined with 100 K data in a monoclinic (C2) space group. This compound with a triterpenoid structure, now confirmed by this study, played an important role in the determination of the structure of lanosterol. The mol-ecules pack in linear O-H⋯O hydrogen-bonded chains along the short axis (b), while parallel chains display weak van der Waals inter-actions that explain the needle-shaped crystal morphology. The structure exhibits disorder of the flexible methyl-heptane chain at one end of the main mol-ecule with a small void around it. Crystals of the compounds were resistant to data collection for decades with the available cameras and Mo Kα radiation single-crystal diffractometer in our laboratory until a new instrument with Cu Kα radiation operating at 100 K allowed the structure to be solved and refined.

Ferroelectricity of a Tetraphenylporphyrin Derivative Bearing −CONHC14H29 Chains at 500 K

Optical properties of porphyrin derivatives were used to fabricate an artificial light-harvesting system. The introduction of a N–H···O═ hydrogen-bonding alkylamide chain (−CONHCnH2n+1) into a functional π-system is among the useful approaches to design multifunctional supramolecular assemblies. The tetraphenylporphyrin derivative bearing four −CONHC14H29 chains (1) shows the successive and reversible phase transition behavior of S1–S2 at 338 K, S2–Colr at 444 K, and Colr–I (isotropic liquid) at 564 K, where a fluidic discotic rectangular columnar (Colr) liquid crystal phase was observed in a wide temperature range of 444–564 K before melting. The one-dimensional columnar molecular assembly of (1)∞ was constructed using a simultaneous operation of N–H···O═ hydrogen-bonding and π-stacking interactions. Temperature (T)- and frequency (f)-dependent dielectric constants of 1 indicated characteristic dielectric enhancement at higher-T and lower-f conditions above 500 K because of the thermally activated motion...

Complexes of palladium(II) chloride with 3-(pyrazol-1-yl)propanamide (PPA) and related ligands

Four new derivatives of the versatile polyfunctional ligands 3-(pyrazol-1-yl)propanamide (1, = PPA) and 3-(3,5-dimethylpyrazol-1-yl)-propanamide (2, = Me2PPA) have been prepared, in which one of the amide hydrogens on 1 and 2 is formally replaced by alkyl residues. X-Ray diffraction studies revealed that, in contrast to 1 and 2, the N-isopropyl substituted derivatives 3 and 4 form supramolecular hydrogen-bonded chains rather than two-dimensional arrays, and the N-(2-methyl-4-oxypentan-2-yl) (=MOP) substituted compounds 5 and 6 exist as cyclic dimers in the solid state. Reactions of PdCl2(COD) (COD = 1,5-cyclooctadiene) with 2 equiv. of the corresponding ligands 1–6 in all cases afforded trans-PdCl2(L)2 complexes (7–12). X-ray crystal structure determinations of 8, and 10–12 revealed κN-monodentate coordination of the PPA-type ligands.

Nanoscale Effects in One-Dimensional Columnar Supramolecular Ferroelectrics.

Organic ferroelectrics have been actively developed with the goal of fabricating environmentally friendly and low-cost memory devices. The remanent polarization of hydrogen-bonded organic ferroelectrics approaches that of the inorganic ones. Nanoscale fabrication of organic ferroelectrics is an essential aspect of high-density memory devices. A pyrene derivative with four tetradecylamide (-CONHC14 H29 ) chains (1) formed an amide-type N-H⋅⋅⋅O hydrogen-bonded one-dimensional (1D) column, which demonstrated ferroelectricity in the discotic hexagonal columnar (Colh ) liquid crystalline phase through the inversion of the orientation of the hydrogen-bonded chains. On the contrary, similar chiral pyrene derivatives bearing 3,7-dimethyl-1-octhylamide chains (S-2 and R-2) did not indicate the Colh phase and ferroelectricity. Homogeneous mixed liquid crystals (1)1-x (S-2)x (i.e., between the ferroelectric 1 and the non-ferroelectric S-2) enable the control of the nanoscale aggregation state of the organic ferroelectrics, resulting in a nanoscale effect of the 1D supramolecular ferroelectrics. Ferroelectric mixed liquid crystals (1)1-x (S-2)x were observed at x≦0.03, where one S-2 molecule was inserted after every thirty-three 1 molecule in the mixed liquid crystal (1)33 (S-2). An average (1)34 length of approximately 12 nm was required to maintain the 1D ferroelectricity, which was similar to the nanoscale limit of inorganic ferroelectrics, such as hafnium oxide thin film (≈15 nm).

X-Ray Crystal Structures and Organogelator Properties of (R)-9-Hydroxystearic Acid.

(R)-9-hydroxystearic acid, (R)-9-HSA, is a chiral nonracemic hydroxyacid of natural origin possessing interesting properties as an antiproliferative agent against different cancer types. Considering its potential application for medical and pharmaceutical purposes, the structures and rheological properties of (R)-9-HSA were investigated. Oscillatory rheology measurements reveal that (R)-9-HSA gels only paraffin oil, with less efficiency and thermal stability than its positional isomer (R)-12-HSA. Conversely, (R)-9-HSA affords crystals from methanol, acetonitrile, and carbon tetrachloride. The single crystal structures obtained both at 293 K and 100 K show non-centrosymmetric twisted carboxylic acid dimers linked at the midchain OHs into long, unidirectional chains of hydrogen bonds, owing to head-tail ordering of the molecules. Synchrotron X-ray powder diffraction experiments, performed on the solids obtained from different solvents, show the occurrence of polymorphism in paraffin oil and through thermal treatment of the solid from methanol.

Structure and spectroscopy of the supercapacitor material hydrous ruthenium oxide, RuO2·xH2o, by neutron scattering*

Hydrous ruthenium dioxide, RuO2·xH2O, is a material of active investigation as an electrode material for supercapacitors. A combination of elastic and inelastic neutron scattering together with thermal gravimetric studies and DFT calculations have provided new insight into the nature of the surface species present on RuO2·xH2O. Our results confirm that hydrous ruthenium oxide is a nanocrystalline material consisting of a core of RuO2. We show that the surface consists largely of Ru–OH with small amounts of water hydrogen-bonded to the surface. The hydroxyls are stable up to ∼200°C, i.e. over the composition range x = 0.2–2. The optimal supercapacitor material has x = 0.5–0.7, and in this range, the surface is fully hydroxylated. This provides a route for the proton transport: a proton can attach to a surface hydroxyl to generate coordinated water, proton transport then occurs along the hydrogen-bonded chain by a Grotthuss mechanism.

The complexation of 2,4-dinitrophenol with basic drugs: Acid + base = salt

Different drugs containing a basic nitrogen atom were crystallised with 2,4-dinitrophenol to study the mode of complexation in search of an antidote to 2,4-dinitrophenol poisoning. The protonated forms of quininium, quinidinium and trazodonium form N–H···O hydrogen bonds to the deprotonated O atom of the 2,4-dinitrophenolate anion, whereas haloperidolium forms a bifurcated N–H···(O,O) hydrogen bond to the deprotonated O atom of 2,4-dinitrophenol and an O atom of the adjacent nitro group. Hydrogen-bonded chains occur in the quininium, quinidinium and haloperidolium crystal structures, whereas the trazodonium structure consists of ion pairs. These results are discussed with a view to lowering the toxicity of 2,4-dinitrophenol in the body in the case of an overdose.

Inter-molecular hydrogen bonding in isostructural pincer complexes [OH-( t-BuPOCOP t-Bu)MCl] (M = Pd and Pt).

In the crystal structure of the isostructural title compounds, namely {2,6-bis-[(di-tert-butyl-phosphan-yl)-oxy]-4-hy-droxy-phen-yl}chlorido-palladium(II), [Pd(C22H39O3P2)Cl], 1, and {2,6-bis-[(di-tert-butyl-phosphan-yl)-oxy]-4-hy-droxy-phen-yl}chlorido-platinum(II), [Pt(C22H39O3P2)Cl], 2, the metal centres are coordinated in a distorted square-planar fashion by the POCOP pincer fragment and the chloride ligand. Both complexes form strong hydrogen-bonded chain structures through an inter-action of the OH group in the 4-position of the aromatic POCOP backbone with the halide ligand.

Crystal structures of butyl 2-amino-5-hy-droxy-4-(4-nitro-phen-yl)benzo-furan-3-carboxyl-ate and 2-meth-oxy-ethyl 2-amino-5-hy-droxy-4-(4-nitro-phen-yl)benzo-furan-3-carboxyl-ate.

The title benzo-furan derivatives 2-amino-5-hy-droxy-4-(4-nitro-phen-yl)benzo-furan-3-carboxyl-ate (BF1), C19H18N2O6, and 2-meth-oxy-ethyl 2-amino-5-hy-droxy-4-(4-nitro-phen-yl)benzo-furan-3-carboxyl-ate (BF2), C18H16N2O7, recently attracted attention because of their promising anti-tumoral activity. BF1 crystallizes in the space group P . BF2 in the space group P21/c. The nitro-phenyl group is inclined to benzo-furan moiety with a dihedral angle between their mean planes of 69.2 (2)° in BF1 and 60.20 (6)° in BF2. A common feature in the mol-ecular structures of BF1 and BF2 is the intra-molecular N-H⋯Ocarbon-yl hydrogen bond. In the crystal of BF1, the mol-ecules are linked head-to-tail into a one-dimensional hydrogen-bonding pattern along the a-axis direction. In BF2, pairs of head-to-tail hydrogen-bonded chains of mol-ecules along the b-axis direction are linked by O-H⋯Ometh-oxy hydrogen bonds. In BF1, the butyl group is disordered over two orientations with occupancies of 0.557 (13) and 0.443 (13).

Side chain to main chain hydrogen bonds stabilize a polyglutamine helix in a transcription factor

Polyglutamine (polyQ) tracts are regions of low sequence complexity frequently found in transcription factors. Tract length often correlates with transcriptional activity and expansion beyond specific thresholds in certain human proteins is the cause of polyQ disorders. To study the structural basis of the association between tract length, transcriptional activity and disease, we addressed how the conformation of the polyQ tract of the androgen receptor, associated with spinobulbar muscular atrophy (SBMA), depends on its length. Here we report that this sequence folds into a helical structure stabilized by unconventional hydrogen bonds between glutamine side chains and main chain carbonyl groups, and that its helicity directly correlates with tract length. These unusual hydrogen bonds are bifurcate with the conventional hydrogen bonds stabilizing α-helices. Our findings suggest a plausible rationale for the association between polyQ tract length and androgen receptor transcriptional activity and have implications for establishing the mechanistic basis of SBMA.

Using Graphs of Dynamic Hydrogen-Bond Networks To Dissect Conformational Coupling in a Protein Motor.

DExD/H-box proteins are soluble enzymes that couple binding and hydrolysis of adenosine triphosphate (ATP) with reactions involving RNA metabolism or bind and push newly synthesized proteins across bacterial cell membranes. Knowledge of the reaction mechanism of these enzymes could help the development of new therapeutics. In order to explore the mechanism of long-distance conformational coupling in SecA, the DEAD-box motor of the Sec protein secretion in bacteria, we implemented algorithms that provide simplified graph representations of the protein's dynamic hydrogen-bond networks. We find that mutations near the nucleotide-binding site or changes of the nucleotide-binding state of SecA associate with altered dynamics at the preprotein binding domain and identify extended networks of hydrogen bonds that connect the active site of SecA to the region where SecA binds newly synthesized secretory proteins. Water molecules participate in hydrogen-bonded water chains that bridge functional domains of SecA and could contribute to long-distance conformational coupling.

Synthesis, Crystal Structure and Thermal Property of Two New Coordination Polymers with Ligands Containing Both N and O Donors

Two new metal–organic coordination polymer frameworks formulated as, {[Co(nta)]·H3O+}n (1), and {[Zn(ina)Cl2]·H3O+·H2O}n (2) (nta = nitriliotriacetic acid, ina = isonicotinate), have been synthesized under mild conditions and characterized by elemental analyses, IR spectrum, PXRD, thermal gravimetric analysis (TG) and single-crystal X-ray diffraction. Complex 1 crystallizes in the orthorhombic space group P2(1)2(1)2(1) with unit cell parameters a = 8.403(4) A, b = 10.165(5) A, c = 11.230 A, β = 90, V = 959.3(9) A3. Complex 2 crystallizes in the monoclinic space group P2(1)/c with unit cell parameters a = 7.1334(13) A, b = 22.369(4) A, c = 7.0089(13) A, β = 101.099(2), V = 1097.5(3) A3. In fact, 1 is a new 3D cobalt complex with the nta ligands acted as bridges to form network polymer. Each nta ligand bonds to three cobalt ions, and each cobalt ion coordinates with three nta ligands in different directions. 2 displays a new 1D zigzag chain linked by ina ligand and an interesting 1D hydrogen-bond infinite chain consists of seven-membered rings and four-membered rings. These chains are further linked to generate a new 3D framework. Two novel metal–organic coordination polymer frameworks have been synthesized under mild conditions and characterized by elemental analyses, IR spectrum, PXRD, thermal gravimetric analysis (TG) and single-crystal X-ray diffraction.

Hydrogen-Bonded Polyrotaxane Cation Structure in Nickel Dithiolate Anion Radical Salts: Ferromagnetic and Semiconducting Behavior Associated with Structural Phase Transition.

The pseudo-polyrotaxane structure of [(H-bpy+ )- (DB-24-crown-8)]∞ (H-bpy+ = monoprotonated 4,4-bipyridinium; DB-24-crown-8 = dibenzo-24-crown-8) has been incorporated into the anion radical salt [Ni(dmit)2 ]- (dmit2- = 1,3-dithiole-2-thione-4,5-dithiolate). (H-bpy+ )(DB-24-crown-8)[Ni(dmit)2 ]- crystallized as two polymorphs, crystals 1 and 2. Crystal 1 was found to have a lower density and looser packing structure in which H-bpy+ forms a one-dimensional hydrogen-bonding chain that passes though the crown ether ring of DB-24-crown-8. DB-24-crown-8 adopts a U-shaped conformation in which two phenylene rings sandwich one of the pyridyl rings of H-bpy+ to stabilize the structure. The [Ni(dmit)2 ]- anions are arranged in a layer parallel to the (10) plane with uniform side-by-side interactions. A structural phase transition was observed at 235 K, accompanied by ordering of the polyrotaxane structure. In crystal 1, at 173 K, H-bpy+ is twisted around the central C-C bond, which perturbs the arrangement of [Ni(dmit)2 ]- through short C-H⋅⋅⋅S contacts. As a result, the semiconducting behavior, with an activation energy of 0.21 eV, becomes insulating below 235 K. The crystal exhibits ferromagnetic interactions because of the weak side-by-side interactions between [Ni(dmit)2 ]- anions. Crystal 2 has a similar pseudo-polyrotaxane structure but showed no phase transition. This suggests that the looser crystal packing in crystal 1 induces the structural change of the pseudo-polyrotaxane, perturbing the electron system of [Ni(dmit)2 ]- .

C-H···O Hydrogen Bond Anchored Water Bridge in 1,2,4,5-Tetracyanobenzene-Water Clusters.

The hydrogen-bonded chain of water molecules is known to play a very important role in proton/H transfer in chemistry and biology. This kind of water chain mainly starts from a conventional hydrogen bond (HB) donor/acceptor site. Here, we report the experimental evidence of water chain formation on an unconventional C-H HB donor site in 1,2,4,5-tetracyanobenzene (TCNB). Laser-induced fluorescence (LIF) spectra and fluorescence dip IR (FDIR) spectra of 1: n ( n = 1-3) clusters of TCNB with water prepared in a supersonic molecular jet are presented. Quantum chemical calculations of several intuitive conformers of 1: n ( n = 1-3) clusters were performed, and the computed IR spectra were compared with the experimental FDIR spectra in order to get the structural information on the experimentally observed clusters. We find that the first water molecule binds to the C-H moiety of TCNB (1:1 cluster) and the subsequent water molecules form a water chain (1:2 and 1:3 clusters) that constitutes a bridge between the C-H and the proximal -CN moiety of TCNB, forming a cyclic ring structure. NBO calculations show that upon addition of water molecules significant change in the charge distribution takes place, mainly on the atoms which are involved in cyclic ring structure. This redistribution of charges causes a cooperativity effect in the higher water clusters of TCNB.

Drastic Change in Electronic Transition upon Hydrogen Bond Network Switching in 3-Aminopyridine-(H2O) n Clusters.

The hydration structures of 3-aminopyridine (3AP)-(H2O) n ( n = 2-4) in supersonic jets have been investigated by measuring the electronic and vibrational spectra with the aid of quantum chemical calculations. The S1-S0 electronic transition of 3AP-(H2O)2 is observed at a slightly red-shifted position from 3AP-(H2O)1, while further hydration induces drastic red shifts and complicated vibrational structures. We assign the cluster structures of 3AP-(H2O)2 as a cyclic structure composed of the homodromic hydrogen bond (H-bond) chain connecting the pyridyl CH bond acting as the proton donor toward a pyridyl nitrogen acceptor. For 3AP-(H2O) n ( n = 3, 4), on the other hand, the initial donor site in the H-bond network changes from a pyridyl CH group to an amino group. The observed red shift derived from H-bond network switching can be reproduced very well with the S1-S0 origin band estimation obtained by applying geometry optimization and subsequent harmonic vibrational analysis of (TD-)DFT calculations to each electronic state of the isomer structure. It is suggested that the drastic red shift of the electronic transition upon H-bond network switching is due to a much more stabilized "quinoid-like" structure in the ππ* state by the H-bond formation of an amino group.

Distortion and a Strong Hydrogen Bond in the Retinal Chromophore Enable Sodium-Ion Transport by the Sodium-Ion Pump KR2.

We conducted a comprehensive time-resolved resonance Raman spectroscopy study of the structures of the retinal chromophore during the photocycle of the sodium-ion pump Krokinobacter rhodopsin 2 (KR2). We succeeded in determining the structure of the chromophore in the unphotolyzed state and in the K, L, M, and O intermediates, by overcoming the problem that only a small fraction of the M intermediate is accumulated in the KR2 photocycle. The Schiff base in the retinal chromophore forms a strong hydrogen bond in the unphotolyzed state and in the K, L, and O intermediates and is deprotonated in the M intermediate. Formation of this strong hydrogen bond facilitates deprotonation of the Schiff base, which is necessary for the sodium ion to move past the Schiff base. The polyene chain in the chromophore of KR2 is twisted in all of the states of the photocycle: the portion near the Schiff base is largely twisted in the unphotolyzed state and in the K intermediate, whereas the middle portion of the polyene chain becomes largely twisted in the L, M, and O intermediates. During the photocycle, the twisted structure of the polyene chain and strong hydrogen bond at the Schiff base are advantageous for transient relocation of the Schiff base proton. The obtained resonance Raman data clarified the unique structural features of the KR2 chromophore, which are not accessible by other methods.

Proton conductivity of glycosaminoglycans.

Proton conductivity is important in many natural phenomena including oxidative phosphorylation in mitochondria and archaea, uncoupling membrane potentials by the antibiotic Gramicidin, and proton actuated bioluminescence in dinoflagellate. In all of these phenomena, the conduction of protons occurs along chains of hydrogen bonds between water and hydrophilic residues. These chains of hydrogen bonds are also present in many hydrated biopolymers and macromolecule including collagen, keratin, chitosan, and various proteins such as reflectin. All of these materials are also proton conductors. Recently, our group has discovered that the jelly found in the Ampullae of Lorenzini- shark’s electro-sensing organs- is the highest naturally occurring proton conducting substance. The jelly has a complex composition, but we proposed that the conductivity is due to the glycosaminoglycan keratan sulfate (KS). Here we measure the proton conductivity of hydrated keratan sulfate purified from Bovine Cornea. PdHx contacts at 0.50 ± 0.11 mS cm -1, which is consistent to that of Ampullae of Lorenzini jelly at 2 ± 1 mS cm -1. Proton conductivity, albeit with lower values, is also shared by other glycosaminoglycans with similar chemical structures including dermatan sulfate, chondroitin sulfate A, heparan sulfate, and hyaluronic acid. This observation supports the relationship between proton conductivity and the chemical structure of biopolymers.

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...

Salt formation of two BCS II drugs (indomethacin and naproxen) with (1R, 2R)-1,2-diphenylethylenediamine: Crystal structures, solubility and thermodynamics analysis

Indomethacin (Indo) and naproxen (Nap) belong to Biopharmaceutical Classification System (BCS) class II drugs, which permeate membranes well but are poorly soluble. Two pharmaceutical salts hydrate of Indo and Nap with (1R,2R)-1,2-diphenylethylenediamine (DPEN) were obtained using solution crystallization. Both salts, (DPEN)2·(Indo)2·(H2O)2 and (DPEN)1·(Nap)1·(H2O)0.5, were characterised using various solid-state characterisation techniques such as single crystal X-ray diffraction (SCXRD), powder X-ray diffraction (PXRD), thermogravimetric analysis (TGA), differential scanning calorimetry (DSC), and Raman spectra. The structure analysis shows that DPEN is monocation as only one amine is protonated into ammonium. The Indo, DPEN and water molecules form one-dimensional hydrogen bond chains through extensive NH⋯O, NH⋯N and OH⋯N interactions. The solubility study shows that the two salts are more soluble in pH 1.2, 4.5 and 6.8 buffer mediums compared with pure raw materials. Solubility thermodynamics calculation was carried out to further understand the solubility properties of two salts.