Hydrogen-bonding Functionality Research Articles

Catalytic Carbon−Hydrogen Bond Functionalization in an Ionic Liquid Medium

The functionalization of unreactive C−H bonds of several hydrocarbons has been achieved at room temperature by the formal insertion of carbene/CHCO2Et units (from ethyl diazoacetate) into such bonds, using copper-based catalysts in a biphasic reaction medium (ionic liquid-hydrocarbon). Catalyst and product separation has been carried out easily, and the recycle of the catalyst for five cycles has been achieved without any loss of catalytic activity.

3D-, 2D- and 1D-supramolecular structures of {Zn[S2CN(CH2CH2OH)R]2}2 and their {Zn[S2CN(CH2CH2OH)R]2}2(4,4′-bipyridine) adducts for R = CH2CH2OH, Me or Et: polymorphism and pseudo-polymorphism

Supramolecular aggregation in the binary zinc dithiocarbamates, in which the dithiocarbamate ligands carry hydrogen-bonding functionality, i.e. {Zn[S2CN(CH2CH2OH)R]2}2, leads to 3D-, 1D- and 2D-architectures for R = CH2CH2OH, Et and Me, respectively. For R = CH2CH2OH, two polymorphs are found, both with 3D-network structures, but constructed from undulating (orthorhombic form) or flattened (monoclinic) layers. Linear chains are found for R = Et where molecules associate head-to-head. The intervention of solvent methanol in the R = Me structure provides additional links between molecules to allow the formation of a 2D-array. In their 4,4-bipyridine adducts, {Zn[S2CN(CH2CH2OH)R]2}2(4,4′-bipyridine), 3D-, 1D- and 2D-architectures are also found. 3D-networks are found for the R = CH2CH2OH and Et derivatives. For the latter compound, solvent methanol in its pseudopolymorph disrupts the 3D-network so that a 1D-supramolecular chain is found. Finally, in the R = Me structure, orthogonally inclined 2D-arrays are interpenetrated to form a 3D-network.

Prediction of Physicochemical Properties of Organic Compounds from 2D Molecular Structure – Fragment Methods vs. LFER Models

A large number of models is available to predict physicochemical properties directly from the two-dimensional molecular structure. An alternative to conventional fragment methods is given by linear free-energy relationships (LFERs) employing Abraham parameters. The latter have a solid mechanistic background, but a drawback in practice is the limited availability of Abraham parameters for substances of interest. As a consequence, more complex compounds typically require the estimation of Abraham parameters from the chemical structure. Comparative analysis of prediction methods for Henry's law constant and sorption to soil organic matter shows that at present, fragment methods are superior to the LFER approach when employing calculated Abraham parameters. For the subset of typically more simple compounds with experimental Abraham parameters, the respective LFERs are competitive to general-purpose fragment models. The discussion includes analyses of compound subsets without and with hydrogen bond functionalities, and of the impact of structural complexity on the model performance.

Normal coordinates analyses of β- d-allose and α- d-talose in the crystalline state

IR and Raman spectra of β- d-allose, α- d-talose and β- d-allose O-D 5 have been recorded in the 4000–400 cm −1 and in the 4000–20 cm −1 regions. These spectra constitute the experimental support that allows to reproduce theoretically the vibrational frequencies and to establish a force field for these saccharides through a normal coordinate analysis. For this purpose, a modified UBSFF has been combined with an intermolecular potential energy function that includes the Van der Walls interactions, the electrostatic terms, and an explicit hydrogen bond function. The initial force field parameters are derived either from those of d-glucose or d-galactose and are fitted so as to obtain a good agreement between the calculated and the observed frequencies. The obtained results reproduce the experimental frequencies and in order to test the validity of the obtained force field, it has been applied to β- d-allose O-D 5.

Imino Diels–Alder adducts. XII. Two pyrano[3,2-c]quinolines

The crystal structures of pyranoquinolines 9-fluoro-5-phenyl-3,4,4a,5,6,10b-hexahydro-2H-pyrano[3,2-c]quinoline, C18H18FNO, and 9-methyl-5-phenyl-3,4,4a,5,6,10b-hexahydro-2H-pyrano[3,2-c]quinoline, C19H21NO, are isomorphous. In both structures, the pyran ring is exo to the six-membered N-heterocyclic ring formed in the cycloaddition step. The torsion angles across the phenyl linkage for the two structures are -91.2 (1) and -88.3 (2) degrees. The striking feature in both crystal packings is that they do not contain the expected conventional hydrogen bonds, in spite of the presence of good hydrogen-bonding functionalities. Possible C-H...pi interactions are, however, observed.

Cooperative End-to-End and Lateral Hydrogen-Bonding Motifs in Supramolecular Thermoplastic Elastomers

To a large extent, the mechanical properties of polymers are determined by the strength of the physical interactions between chains. Thermoplastic elastomers (TPE’s) make sophisticated use of reversible physical interactions.1 They consist of polymer chains in which strongly interacting segments alternate with weakly interacting segments to give rise to microphase-separated materials with a soft block/hard block morphology. When the hard blocks contain urethane and/or urea groups, strong and specific hydrogen-bonding interactions2 lead to useful properties, such as a high modulus for a given hard block content. In recent years, highly directional physical interactions have been applied in a fundamentally different way to form supramolecular polymers.3 In this novel class of materials, endfunctionalization of unimers with functional groups that associate via noncovalent interactions such as multiple hydrogen bonds4,5 or coordinative bonds6 results in a strong increase of the virtual molecular weight and in concurrent changes of mechanical and rheological properties. The use of directional hydrogen bonding within the hard blocks of TPE’s has been studied by Stadler and co-workers,7 who used telechelic hydrogen-bonded polyisobutylenes with relatively weak end-to-end interactions between urazole groups and between benzoic acid groups. Recently, Bouteiller et al.8 have studied poly(dimethylsiloxane)s with bisurea end groups which aggregate laterally. The authors concluded that aggregation of the end groups into 3-D crystalline domains results in elastomeric behavior, while the formation of hydrogen bonds without crystallization was not sufficient to obtain tensile properties. Similar conclusions were drawn by Rowan et al.,9 who noticed that even very weak end-to end interactions can be used to obtain polymers with film-forming properties when the end groups phase segregate. Here, we study the effect of combining very strong end-toend association via ureidopyrimidinone (UPy) quadruple hydrogen bonding10 and directional lateral aggregation via the urea (U) and urethane (T) hydrogen bonding motifs11 to give supramolecular thermoplastic elastomers with 1-D aggregation of dimerized end groups. Hydroxy-telechelic poly(ethylene butylene) (PEB, Mn ) 3500 g/mol, Mw/Mn ) 1.06, degree of functionalization 1.92) was functionalized with lateral hydrogen-bonding functionalities (UU-PEB-U-U and U-T-PEB-T-U), with end-to-end hydrogenbonding functionalities (UPy-PEB-UPy), and functionalized with both lateral and end-to-end functionalities (UPy-U-PEB-U-UPy and the previously reported5 UPy-T-PEB-T-UPy) (Scheme 1). The resulting materials were characterized with DSC, AFM, dynamic mechanical measurements, and tensile testing. The parent hydroxy-telechelic PEB is a liquid at room temperature which shows purely viscous behavior in oscillatory shear experiments. Incorporation at the chain ends of functional groups capable of lateral aggregation via 3 or 4 hydrogen bonds leads to the formation of elastic solids, with melting points that increases from 45 °C for U-T-PEB-T-U to 129 °C for the U-UPEB-U-U material. The former is a single segment of a segmented, PEB-based poly(urethane-urea) recently reported by Wilkes et al.,2b while the latter material can be considered a PEB analogue of the bisurea-functionalized PDMS reported by Bouteiller.8 In line with the highly directional nature of the hydrogen bonding of UPy moieties, direct functionalization of PEB with the UPy quadruple hydrogen bonding unit in UPyPEB-UPy gives rise to a noticeable increase in viscosity at 40 °C from 10 to 7 × 103 Pa‚s, but it does not lead to the formation of a material with a discernible melting point. The viscosity changes are in line with end-to-end linking of PEB by directional quadruple hydrogen bonds between UPy functional groups, considering that the degree of functionalization of 1.92 of the starting material limits the average number of end-linked unimers to ∼50. A master curve of oscillatory shear experiments on UPy-PEBUPy (Figure 1) confirms the directional end-to-end nature of UPy-UPy hydrogen bonding as the storage and loss moduli show terminal relaxation behavior with slopes of 0.96 and 2.05, demonstrating the absence of long-lived lateral interactions. Nevertheless, the formation of supramolecular polymer chains by linear association of unimers results in an entanglement network with characteristic lifetime of 1 s at 40 °C, evident from a viscoelastic transition at higher frequencies. A dramatic enhancement of mechanical properties was observed when end-to-end and lateral interactions were combined in UPy-U-PEB-U-UPy. In contrast to UPy-PEB-UPy, this material is an elastic solid, with a melting point of 129 °C. The * Corresponding authors. E-mail: r.p.sijbesma@tue.nl; e.w.meijer@tue.nl. Scheme 1. Hydrogen-Bonded Telechelic PEB’s

Fast empirical p Ka prediction by Ewald summation

p K a calculations for macromolecules are normally performed by solving the Poisson–Boltzmann equation, accounting for the different dielectric constants of solvent and solute, as well as the ionic strength. Despite the large number of successful applications, there are some situations where the current algorithms are not suitable: (1) large scale, high-throughput analysis which requires calculations to be completed within a fraction of a second, e.g. when permanently monitoring p K a shifts during a molecular dynamics simulation; (2) prediction of p K as in periodic boundaries, e.g. when reconstructing entire protein crystal unit cells from PDB files, including the correct protonation patterns at experimental pH. Such in silico crystals are needed by ‘self-parameterizing’ molecular dynamics force fields like YASARA YAMBER, that optimize their parameters while energy-minimizing high-resolution protein crystals. To address both problems, we define an empirical equation that expresses the p K a as a function of electrostatic potential, hydrogen bonds and accessible surface area. The electrostatic potential is evaluated by Ewald summation, which captures periodic crystal environments and the uncertainty in atom positions using Gaussian charge densities. The empirical proportionality constants are derived from 217 experimentally determined p K as, and despite its simplicity, this p K a calculation method reaches a high overall jack-knifed accuracy, and is fast enough to be used during a molecular dynamics simulation. A reliable null-model to judge p K a prediction accuracies is also presented.

Alkane Carbon−Hydrogen Bond Functionalization with (NHC)MCl Precatalysts (M = Cu, Au; NHC = N-Heterocyclic Carbene)

Facile alkane functionalization by means of the insertion of :CHCO2Et, from ethyl diazoacetate, into carbon−hydrogen bonds mediated by catalytic amounts of (NHC)MCl (NHC = N-heterocyclic ligand; M = Cu, Au) and a halide scavenger MX has been achieved. This chemistry includes the insertion of the carbene fragment into alkane primary positions with Cu- and Au-based catalysts. The nature of the counterion X and of the NHC ligand have a significant effect on the overall yields and regioselectivity of the reaction.

Supramolecular aggregation in diimine adducts of zinc(ii) dithiophosphates: controlling the formation of monomeric, dimeric, polymeric (zig-zag and helical), and 2-D motifs

The interplay between steric demands of dithiophosphate-bound R groups in Zn(S2P(OR)2)2 on the one hand and the coordination requirements of a variety of di-pyridyl-type bases on the other, is shown to be pivotal in determining supramolecular aggregation patterns in a series of their adducts. Thus, the combination of sterically demanding cyclohexyl groups and the congested trans-1,2-bis(2-pyridyl)ethylene ligand leads to a mononuclear species, but replacing the cyclohexyl by the less bulky isopropyl group allows for dimer formation in the structure of [Zn(S2P(OiPr)2)2(2-NC5H4C(H)C(H)C5H4N-2)0.5]2; a similar motif is found when pyrazine is the bridging ligand. These molecules aggregate in the solid-state to form chains via C–H⋯O interactions. Zig-zag polymers are found when the somewhat less congested 2,2′-dithiopyridine and bis(4-pyridyl)amine ligands are used as the bridges; the hydrogen-bonding functionality in the latter leads to a 2-D motif. Finally, exploiting the curved nature of the 1,3-bis(4-pyridyl)propane ligand leads to the formation of helical chains.

Influence of Hydrogen-Bonding Substituents on the Cytotoxicity of RAPTA Compounds

A new series of organometallic ruthenium(II)-arene compounds of the type RuCl2(η6-arene)(phosphine) (phosphine = 1,3,5-triaza-7-phosphaadamantane, PTA, and 3,7-diacetly-1,3,7-triaza-5-phosphabicyclo[3.3.1]nonane, DAPTA) with different potential hydrogen-bonding functionalities on the arene ligand have been prepared and studied for their antitumor activity. Cell viability studies using the TS/A mouse adenocarcinoma cancer cell line and the nontumorigenic HBL-100 human mammary cell line, combined with uptake determinations, are compared to the nonfunctionalized analogues, previously shown to be active on solid metastasizing tumors. The reactivity of the functionalized RAPTA compounds with a 14-mer oligonucleotide (established by mass spectrometry) has been rationalized by DFT calculations, which indicate that environmental factors are important.

Alternate synthetic strategy for the preparation of CdS nanoparticles and its exploitation for water splitting

Cadmium sulphide nanoparticles (6–12 nm) are prepared by a precipitation process using different zeolite matrices as templates. The nanoparticles were characterized by UV-Vis, XRD, SEM, TEM and sorptometric techniques. XRD study shows the presence of hexagonal and cubic phases for the nanoparticles whereas in case of the bulk samples only the hexagonal phase is observed. These nanomaterials have been used as catalysts for the photocatalytic decomposition of water. The nanoparticles show a higher hydrogen evolution rate compared to the bulk samples which correlates well with the particle size and surface area. Noble metal (Pt, Pd, Rh, Ru)-loaded samples were subsequently prepared and tested for hydrogen evolution reaction. The presence of Pt metal is found to enhance the hydrogen production rate whereas the hydrogen production rate is retarded in the presence of Ru metal. This has been explained on the basis of metal hydrogen bond, redox potential and work function of the noble metal.

Dibenzotetrathiafulvalene with Amino Groups: New Electron-Donor Molecule with Hydrogen-Bonding Functionalities

Dibenzotetrathiafulvalene (DBTTF) with two amino groups, DADBTTF, has been designed as a new TTF derivative with intermolecular hydrogen-bonding functionalities and synthesized as a stable solid in air. The first oxidation potential of DADBTTF was negatively shifted by 0.24 V compared with that of DBTTF, suggesting a noticeable change in the electronic structure induced by the substitution effect of the two amino groups. The crystal structure of DADBTTF shows the E-type configuration of this molecule and columnar stacking structure through the π…π interaction with interplanar distance of 3.5 Å.

Palladium complexes containing ligands with hydrogen-bonding functionalities. Reactivity and catalytic studies with CO and olefins

The synthesis of the new bidentate N–N ligand 1-(2-(1-(pyridin-2-yl)ethylideneamino)ethyl)-3-ethylurea ( PyUr) with a urea substituent attached to the imine nitrogen is reported. This ligand has been used to form palladium complexes and study the potential influence of the urea group (as a hydrogen bonding unit and a hemilabile ligand) in the insertion of CO and olefins into Pd–C bonds. The reaction of PyUr with [Pd(CH 3)(Cl)(COD)] to yield [Pd(CH 3)Cl( PyUr)] ( 1) is reported. A crystallographic study of this complex was carried out showing that the urea moieties are involved in a series of intermolecular hydrogen bonding interactions. Upon removal of the chloride from the coordination sphere of 1 (by addition of AgBF 4) the urea group of PyUr coordinates to the palladium centre stabilizing an otherwise coordinatively unsaturated complex. The reaction of these complexes with CO to yield [Pd{C( O)CH 3}Cl( PyUr)] ( 3) and [Pd{C( O)CH 3}( PyUr)][BF 4] ( 4) is also discussed. Following on from these reactions, the copolymerization of CO and styrene using 1 as a catalyst was studied and is herein reported. The copolymers synthesized using 1 as a catalyst were obtained in moderate yields and showed to have a narrow size distribution. The same reaction was performed using a palladium complex coordinated by an analogous pyridine ligand but without a hydrogen bonding substituent. The results of the copolymerization reactions showed that, although slightly better yields and larger molecular weights were obtained with the PyUr-containing catalyst, the hydrogen bonding groups in PyUr have little influence on the course of the reaction. To explore further the reactivity of the palladium complexes, the reaction between [Pd(CH 3)Cl( PyUr)][BF 4] ( 2) and CH 2 CHCH 2OH was carried out to yield the allyl complex [Pd(η 3-CH 2CHCH 2)( PyUr)] ( 6). The crystal structure of this complex is also reported.

A Mechanism for Phosphate Hardening and Prospects for the Use of Metal Phosphate Materials (A Review). Part I. The Nature of Hydrogen Bonding and Its Function in the Mechanism of Phosphate Hardening

The physical chemistry of multistep hardening of phosphate bonding materials is considered. The function of hydrogen bonds in the phosphate hardening mechanism and their effect on the adhesive properties of phosphate bonding materials are discussed. Techniques for enhancing the adhesive properties of phosphate binders using powdered oxides, hydroxides, and salts and their involvement in acid-base reactions are considered. Bonding materials for nonfired refractories, corrosion-resistance coatings and mortars, and areas for their potential applications are proposed.

Supercooled Water in PVA Matrixes. II. A Molecular Dynamics Simulation Study and Comparison with QENS Results

Molecular dynamics (MD) simulations were carried out to elucidate the dynamic behavior of water confined in poly(vinyl alcohol), PVA, hydrogels. Model topology is supported by experimental network parameters, and simulation results are compared to an incoherent quasielastic neutron scattering (QENS) investigation carried out on PVA hydrogels. From the QENS dynamic scattering law (part I), a random jump model was adopted for the description of water diffusion to extract a microscopic diffusion coefficient and a residence time between two "jumps". In the present work, consistently with this framework, water diffusion parameters as diffusion coefficients and residence times have been evaluated using the mean square displacement of water in a time window of 10 ps and the time autocorrelation function of water hydrogen bonds. The calculated parameters are in good agreement with the experimental ones, giving confidence to this approach. Further developments are in progress to take into account a more realistic description of hydrogel structure in the molecular dynamics simulations.

Hydrogen-Bonded Networks Featuring Yttrium(III) Complexes of N,N’-Dimethylurea (DMU): Preparation and Characterization of [Y(DMU)6][YCl6] and [Y(NO3)3(DMU)3

In order to examine the possibility of using yttrium(III) in the crystal engineering of hydrogenbonded coordination complexes and to compare the molecular and supramolecular YIII/Cl3 or NO3 -/DMU chemistry with the already well-developed LnIII/Cl− or NO3 −/DMU chemistry (LnIII = lanthanide, DMU = N,N’-dimethylurea), compounds [Y(DMU)6][YCl6] (1) and [Y(NO3)3(DMU)3] (2) have been prepared. The structures of both compounds have been determined by single-crystal Xray diffraction. The structure of 1 consists of octahedral [Y(DMU)6]3+ and [YCl6]3− ions. The YIII ion in 2 is nine-coordinate and ligation is provided by three O-bonded DMU ligands and three bidentate chelating nitrato groups; the coordination polyhedron about the metal can be viewed as a distorted, monocapped square antiprism. The [Y(DMU)6]3+ cations and [YCl6]3− anions self-assemble to form a hydrogen-bonded 3D architecture in 1. Most of the hydrogen-bonding functionalities on the components of 2 create also a 3D network. Two motifs of interionic/intramolecular hydrogen-bonds have been observed: N-H···Cl in 1 and N-H···O(NO3 −) in 2. The IR data are discussed in terms of the nature of bonding and the structures of the two complexes

Functional models for catechol dioxygenases: Iron(III) complexes of cis-facially coordinating linear 3N ligands

A series of 1:1 iron(III) complexes of simple and sterically hindered tridentate 3N donor ligands have been synthesized and studied as functional models for catechol dioxygenases. All of them are of the type [FeLCl 3], where L is bis(pyrid-2-yl-methyl)amine (L1), N,N-bis(benzimidazol-2-ylmethyl)amine (L2), N-methyl- N′-(pyrid-2-ylmethyl)ethylenediamine (L3), N,N-dimethyl- N′-(pyrid-2-ylmethyl)-ethylenediamine (L4) and N-phenyl- N′-(pyrid-2-ylmethyl)ethylenediamine (L5). They have been characterised by spectral and electrochemical methods. The X-ray crystal structure of the complex [Fe(L4)Cl 3] has been successfully determined. The complex crystallizes in the triclinic space group P 1 ¯ with a = 7.250(6), b = 8.284(3), c = 12.409(4) Å, α = 80.84(3)°, β = 86.76(6)°, γ = 72.09(7)° and Z = 2. It possesses a distorted octahedral geometry in which the L4 ligand is cis-facially coordinated to iron(III) and the chloride ions occupy the remaining coordination sites. The systematic variation in the ligand donor atom type significantly influences the Lewis acidity of the iron(III) center and hence the binding interaction of the complexes with simple and substituted catechols. The spectroscopic and electrochemical properties of the catecholate complexes generated in situ have been investigated. All the complexes catalyze mainly the oxidative intradiol cleavage of 3,5-di- tert-butylcatechol (H 2DBC) in the presence of dioxygen, which is unexpected of the cis-facial coordination of the ligands. The rate of intradiol catechol cleavage reaction depends upon the Lewis acidity of iron(III) center and steric demand and hydrogen-bonding functionalities of the ligands. Interestingly, the electron-sink property of N-phenyl substituent in [Fe(L5)Cl 3] complex leads to enhancement in rate of cleavage. All these observations provide support to the substrate activation mechanism proposed for intradiol-cleaving enzymes.

Supramolecular associations in binary antimony(iii) dithiocarbamates: influence of ligand steric bulk, influence on coordination geometry, and competition with hydrogen-bonding

New structural data for molecules of the general formula Sb(S2CNR2)3, with both non-sterically and sterically demanding R groups, complement literature data and allow an assessment of factors dictating supramolecular association. With relatively small R substituents, dimer formation via Sb⋯S secondary interactions is observed. With bulky R groups, Sb⋯S interactions are not possible owing to steric hindrance and C–H⋯S hydrogen-bonding predominates instead, again leading to dimers. In cases where R carries hydrogen-bonding functionality, both Sb⋯S and O–H⋯O co-exist when R is small but Sb⋯S secondary bonding is switched off when R becomes larger. The conclusion of the study is that remote R substituents in molecules of this type are able to dictate modes of supramolecular association, i.e. Sb⋯S versus C–H⋯S, and that the resultant formation of loosely associated dimers facilitates efficient crystal packing.

Crystal and molecular structures of two triorganophosphinegold(I) 2-amino-cyclopent-1-ene-1-carbodithioates

Abstract The molecular structures of Ph3PAu · (S2CC5H6NH2-2) and (4-MeOC6H4)3PAu(S2CC5H6NH2-2) · CH2Cl2 display the expected linear S-Au-P coordination geometries. The hydrogen-bonding functionality in the 1,1-dithiolate ligands, i.e., —NH2 groups, allows for the formation of hydrogen-bonded, i.e., N—H…S, mediated chains in the respective crystal structures.

Structural Variations and Polymorphism of Some Derivatives of 6-Amino-2-phenylsulfonylimino- 1,2-dihydropyridine

Following up from a study of polymorphism in the title compound, 6-amino-2-phenylsulfonylimino-1,2-dihydropyridine, 12 phenyl-substituted derivatives were examined for polymorphism by recrystallization from a large number of solvents. The title compound contains hydrogen bond donor (D) and acceptor sites (A) located in a AADD juxtapositioning. Two structural families that differ in their use of the AADD hydrogen bond functionality may be identified. Methyl and chloro substitution in the ortho position or fluoro substitution in the para position leads to a catemer motif, which is related to the kinetic form of the title molecule. Meta Substitution by methyl and larger substituents in the para position block this structural option. While meta-methyl and para-chloro substitution lead to unique structures, two polymorphs of the para-methyl-substituted derivative could be crystallized and these adopt the dimer arrangement. With the larger bromo, iodo, methoxy, and trifluoromethyl substituents in the para position, dimers arranged into interconnected layers are obtained. These dimer structures are reminiscent of the thermodynamic form of the title compound. It is noteworthy that the majority of derivatives of the title compound fail to show polymorphic behavior, and this shows that our understanding of polymorphism is still far from complete.