Ionic Hydrogen Bonds Research Articles

Crystal structure of a PduO‐type ATP:cobalamin adenosyltransferase from Burkholderia thailandensis

Crystal structure of a PduO‐type ATP:cobalamin adenosyltransferase from <i>Burkholderia thailandensis</i>

Contributions to chromatographic chiral recognition of permethrinic acid stereoisomers by a quinine carbamate chiral selector: evidence from X-ray diffraction, DFT computations, 1H NMR, and thermodynamic studies

A chiral stationary phase (CSP) based on O-9-(2,6-diisopropylphenylcarbamoyl)quinine (DIPPCQN) as a chiral selector (SO) exhibits remarkable stereoselectivity for the four stereoisomers of permethrinic acid, 3-(2,2-dichlorovinyl)-2,2-dimethylcyclopropanecarboxylic acid (DCCA), a precursor and prime metabolite of the pyrethroid-type insecticide permethrin. The four individual isomers of DCCA were crystallized as salts of DIPPCQN for crystal structure analysis to further our understanding of chiral recognition. X-ray diffraction structures revealed that the diastereomeric complexes displayed only minor differences in their geometries with regard to specific binding interactions. The common feature is an ionic hydrogen bond, which holds the SO-selectand (SO–SA) complexes together and fixes the individual ligands in the same single point in the binding pocket of the SO. Stereoselectivity seems to arise from distinct orientations of the cyclopropane ring and/or its substituents, which means that it is most likely the result of a plethora of weak non-covalent interactions (dispersion forces) or different steric environments for the substituents of the distinct guest stereoisomers. Herein, other interactive and discriminative forces are also discussed on the basis of the additivity of SO–SA binding contributions in accordance to a linear-free energy model for chiral distinction. The chiral recognition mechanism as deduced from the diffraction data has been complemented by DFT computations, liquid chromatographic thermodynamic analysis, and 1H NMR spectroscopy measurements. DFT computations (geometry optimization at the Hartree–Fock level and single point energy calculations at the B3LYP level) could correctly reproduce the relative binding strengths for the two enantiomers of cis- and trans-DCCA (ΔΔ H −4.2 and −0.52 kJ mol −1, respectively) and thus the chromatographic elution order of the enantiomers. Liquid chromatographic thermodynamic investigations are in reasonable agreement with the relative trends regarding enantiomer affinity and the difference in enthalpy changes upon complexation. 1H NMR experiments in acetonitrile-D 3 confirmed that the anti- open conformation of the quinine carbamate SO is, like in the solid-state, the preferential binding conformation in solution phase as well. Other interactions than the ionic hydrogen bond could not be derived from 1H NMR measurements and thus, in sharp contrast to X-ray diffraction, the 1H NMR experiments undertaken did not allow to infer stereoselectivity contributions.

1,1′-(Butane-1,4-diyl)diimidazolium dinitrate

In the title compound, C10H16N4 2+·2NO3 −, the organic cation is located around an inversion centre. The imidazolium ring forms a dihedral angle of 62.7 (3)° with the plane defined by the C atoms of the –(CH2)4– aliphatic linker. Two anions bind to the cation via three-centre N—H⋯O hydrogen bonds and thus discrete hydrogen-bonded ion triples are formed. The nitrate is approximately coplanar with the imidazolium ring to which it binds.

Photoelectron spectroscopy of hydrated hexafluorobenzene anions

We present a synergetic experimental/theoretical study of hydrated hexafluorobenzene anions. Experimentally, we measured the anion photoelectron spectra of the anions, C6F6(-)(H2O)n (n=0-2). The spectra show broad peaks, which shift to successively higher electron binding energies with the addition of each water molecule to the hexafluorobenzene anion. Complementing these results, we also conducted density functional calculations which link adiabatic electron affinities to the optimized geometric structures of the negatively charged species and their neutral counterparts. Neutral hexafluorobenzene-water complexes are not thought to be hydrogen bonded. In the case of C6F6(-)(H2O)1, however, its water molecule was found to lie in the plane of the hexafluorobenzene anion, bound by two O-H...F ionic hydrogen bonds. Whereas in the case of C6F6(-)(H2O)2, both water molecules also lie in the plane of and are hydrogen bonded to the hexafluorobenzene anion but on opposite ends. This study and that of Schneider et al. [J. Chem. Phys. 127, 114311 (2007), preceding paper] are in agreement regarding the geometry of C6F6(-)(H2O)1.

Heterogeneous Proton-Bound Dimers with a High Dipole Moment Monomer: How Could We Experimentally Observe These Anomalous Ionic Hydrogen Bonds?

Electronic structure calculations (CBS-QB3 and G3MP2) have been used to predict a suitable method to experimentally observe the anomalous structure which is predicted to exist in a proton-bound dimer with a high dipole moment monomer. The enthalpy associated with forming the proton-bound dimer from its protonated and neutral monomers is shown to be linearly related to the difference in proton affinities which has been observed experimentally. However, unlike previous experimental studies, the linear correlation is not predicted to depend strongly, if at all, on whether the basic sites are C=O, C=N, or O(H) n-donor bases. Thermochemical measurements, then, are probably not the best method to distinguish between the structures of heterogeneous proton-bound dimers. It has been shown that a suitable method to experimentally observe the anomalous structure of proton-bound dimers containing a high dipole moment monomer (or very polar monomer) is by spectroscopic measurement. The O-H+-O asymmetric stretch is probably not the best infrared band to try to correlate with structure. The best band to observe is one which is in a region of the spectrum not masked by other absorptions and is also sensitive to the proximity of the binding proton. For example, it is shown that the methanol-free O-H stretch is very sensitive to the O-H+ bond distance for a series of heterogeneous proton-bound dimers containing methanol. It is predicted that the free O-H stretch of the methanol/acetonitrile proton-bound dimer is more closely related to the O-H stretch in protonated methanol than the O-H stretch in neutral methanol. Observations of these bands should confirm that the proton is closer to methanol in the methanol/acetonitrile proton-bound dimer despite acetonitrile having a higher proton affinity.

Infrared spectroscopy of anionic hydrated fluorobenzenes

We investigate the structural motifs of anionic hydrated fluorobenzenes by infrared photodissociation spectroscopy and density functional theory. Our calculations show that all fluorobenzene anions under investigation are strongly distorted from the neutral planar molecular geometries. In the anions, different F atoms are no longer equivalent, providing structurally different binding sites for water molecules and giving rise to a multitude of low-lying isomers. The absorption bands for hexa- and pentafluorobenzene show that only one isomer for the respective monohydrate complexes is populated in our experiment. For C6F6.-H2O, we can assign these bands to an isomer where water forms a weak double ionic hydrogen bond with two F atoms in the ion, in accord with the results of Bowen et al. [J. Chem. Phys. 127, 014312 (2007), following paper.] The spectroscopic motif of the binary complexes changes slightly with decreasing fluorination of the aromatic anion. For dihydrated hexafluorobenzene anions, several isomers are populated in our experiments, some of which may be due to hydrogen bonding between water molecules.

Synthesis and Crystal Structure of 2,13-Bis(acetamido)-3,14-dimethyl-2,6,13,17-tetraazatricyclo[14,4,01.18,07.12]docosane Tetrachlorocobalt(II)dihydrate

The novel ionic compound [H2bdtd][CoCl4] · 2H2O (1) was prepared by the reaction between CoCl2 and 2,13-bis(acetamido)-3,14-dimethyl-2,6,13,17-tetraazatricyclo[14,4,01.18,07.12]docosane (bdtd) in adjusted to pH 3.0 by 1.0 M HCl and structurally characterized. The crystals are monoclinic C2/c with a = 18.7777(9), b = 9.7356(4), c = 20.0884(9) A, β = 109.6340(10)°, V = 3458.9(3) A3, Z = 4. The dication H2bdtd occupies a special position about an inversion center. The cobalt(II) atom in the anion is in a distorted tetrahedral environment with four chloride ligands. The crystal structure is stabilized by a variety of hydrogen-bonding contacts involving the dication, chloride anions and solvent water molecules. Cyclic voltammetry of [CoCl4]2− anion in 1 undergoes irreversible one-electron reduction to the CoII/CoI. The crystal structure of the ionic compound [H2bdtd][CoCl4] · 2H2O (1) consists of [H2bdtd]2+ cation, [CoCl4]2− anion and water molecules joined together by ionic interaction and hydrogen bonds.

Bis(dicyclohexylammonium 4-hydroxybenzoate)

In the crystal structure of the title compound, 2C12H24N+·2C7H5O3−, the cation is linked to the single-bonded carboxylate O atom of an anion as well as to the double-bonded carbonyl O atom of another anion to form a centrosymmetric hydrogen-bonded ion pair. Adjacent ion pairs are linked through the hydr­oxy group of the anion to produce a honeycomb-like layer structure.

Identification of the Substrate Binding Sites within the Yeast Mitochondrial Citrate Transport Protein

The objective of the present investigation was to identify the substrate binding site(s) within the yeast mitochondrial citrate transport protein (CTP). Our strategy involved kinetically characterizing 30 single-Cys CTP mutants that we had previously constructed based on their hypothesized importance in the structure-based mechanism of this carrier. As part of these studies, a modified transport assay was developed that permitted, for the first time, the accurate determination of K(m) values that were elevated >100-fold compared with the Cys-less control value. We identified 10 single-Cys CTP mutants that displayed sharply elevated K(m) values (i.e. 5 to >300-fold). Each of these mutants displayed V(max) values that were reduced by > or = 98% and resultant catalytic efficiencies that were reduced by > or = 99.9%. Importantly, superposition of this functional data onto the three-dimensional homology-modeled CTP structure, which we previously had developed, revealed that nine of these ten residues form two topographically distinct clusters. Additional modeling showed that: (i) each cluster is capable of forming numerous hydrogen bonds with citrate and (ii) the two clusters are sufficiently distant from one another such that citrate is unlikely to interact with all of these residues at the same time. We deduced from these findings that the CTP contains at least two citrate binding sites per monomer, which are located at increasing depths within the translocation pathway. The identification of these sites, combined with an initial assessment of the citrate-amino acid side-chain interactions that may occur at these sites, substantially extends our understanding of CTP functioning at the molecular level.

A Solid-State NMR Study of Hydrogen-Bonding Networks and Ion Dynamics in Benzimidazole Salts

On the basis of our solid-state NMR characterization of dynamics in two model salts, we draw the analogy to the fuel cell membrane candidate, phosphoric acid-doped poly(benzimidazole), and conclude that phosphate anion dynamics contribute to long-range proton transport, whereas the mobility of the polymer itself is not a contributing factor. This is contrasted with emerging membrane candidates, which rely on fully covalently bonded acid donors and acceptors, and target high-temperature PEM fuel cell operation in the absence of liquid electrolyte. The hydrogen-bonding structures of benzimidazolium phosphate and benzimidazolium methane phosphonate are established using X-ray diffraction paired with solid-state 1H DQF NMR. By comparing the dynamics of the phosphate and methane phosphonate anions with the dynamics of imidazolium and benzimidazolium cations, the relative importance of these processes in proton transport is determined. The imidazolium cation is known to undergo two-site ring reorientation on the millisecond time scale. In contrast, it is shown here that the benzimidazolium rings are immobile in analogous salts, on a time scale extending into the tens of seconds. Therefore, we look to the phosphate anions and demonstrate that the time scale of tetrahedral reorientation is comparably fast (50 ms). Moreover, the 31P CODEX NMR data clearly indicate a four-site jump process. In contrast, the methane phosphonate undergoes a three-site jump on a slower time scale (75 ms). A mechanism for a zigzag pathway of proton transport through the phosphonate salt crystallites is developed based on the 31P CODEX and 1H variable-temperature MAS NMR data.

Crystallographic and conformational analyses of zwitterionic form of (E)-2-methoxy-6-[(2-morpholinoethylimino)methyl]phenolate

The single crystal X-ray diffraction analysis of the title compound, C14H20N2O3, reveals that the structure is adapted to its zwitterionic form and $$R_2^2 (12)$$ centrosymmetric dimers are formed by N+–H···O− type ionic weak hydrogen bonds in the crystal structure. The title compound crystallizes in the triclinic space group P−1 with a = 5.9255(13) A, b = 9.853(3) A, c = 12.248(3) A, α = 101.793(19)°, β = 94.941(17)°, γ = 104.36(2)°, Z = 2, Dx = 1.308 g/cm3, μ (Mo-Kα) = 0.092 mm−1. The structure was solved by direct methods and refined to a final R = 0.0371 for 2183 reflections with I > 2σ (I). The crystal structure is stabilized by N+–H···O− type intra-molecular hydrogen bonds and N+–H···O− type packing interactions referred to as weak hydrogen bonds. To elucidate conformational flexibility of the title molecule, the selected torsion angle is varied from −180° to +180° in every 10° separately and then molecular energy profile is calculated and construed. In addition, charge-population analysis of the crystallographically observed structure confirms its zwitterionic form.

Investigation of the effects of ionic hydrogen bonds (C [dbnd]O −⋯H–C and +N–H⋯ −O [dbnd]C) in crystalline dl-proline by ab initio and DFT calculated NQR parameters

In this paper, we have calculated the nuclear quadrupole resonance (NQR) parameters of the quadrupole nuclei involved in the hydrogen bonds (C O −⋯H–C and +N–H⋯ −O C) in the monomer and pentameric cluster of dl-proline by HF and B3LYP methods and basis sets of 6-311+G ∗ and 6-311++G ∗∗. These computations are performed on the basis of X-ray diffraction structural data of dl-proline. The results indicate that the calculations including hydrogen-bonding (HB) interactions (in pentamer) are in better agreement with the experimental data than those in which these interactions are neglected (in monomer). The quantum chemical calculations show that the intermolecular hydrogen-bonding interactions play an important role in determination of the NQR parameters of 14N, 2H of NH 2 + group and 17O.

Mucoadhesion mechanism of chitosan and thiolated chitosan-poly(isobutyl cyanoacrylate) core-shell nanoparticles

The study is focused on the evaluation of the potential bioadhesive behaviour of chitosan and thiolated chitosan (chitosan-TBA)-coated poly(isobutyl cyanoacrylates) (PIBCA) nanoparticles. Nanoparticles were obtained by radical emulsion polymerisation with chitosan of different molecular weight and with different proportions of chitosan/chitosan-TBA. Mucoadhesion was ex vivo evaluated under static conditions by applying nanoparticle suspensions on rat intestinal mucosal surfaces and evaluating the amount of nanoparticles remaining attached to the mucosa after incubation. The analysis of the results obtained demonstrated that the presence of either chitosan or thiolated chitosan on the PIBCA nanoparticle surface clearly enhanced the mucoadhesion behaviour thanks to non-covalent interactions (ionic interaction and hydrogen bonds) with mucus chains. Both, the molecular weight of chitosan and the proportion of chitosan-TBA in the formulation influenced the nanoparticle hydrodynamic diameter and hence their transport through the mucus layer. Improved interpenetration ability with the mucus chain during the attachment process was suggested for the chitosan of high molecular weight, enhancing the bioadhesiveness of the system. The presence of thiol groups on the nanoparticle surface at high concentration (200×10 −6 μmol SH/cm 2) increased the mucoadhesion capacity of nanoparticles by forming covalent bonds with the cysteine residues of the mucus glycoproteins.

Investigating the Molecular Mechanisms of In-Plane Mechanochemistry on Cantilever Arrays

Free-standing cantilevers, which directly translate specific biochemical reactions into micromechanical motion, have recently attracted much attention as label-free biosensors and micro/nano robotic devices. To exploit this mechanochemical sensing technology, it is essential to develop a fundamental understanding of the origins of surface stress. Here we report a detailed study into the molecular basis of stress generation in aqueous environments focusing on the pH titration of model mercaptohexadecanoic acid self-assembled monolayers (SAMs), using in situ reference cantilevers coated with nonionizable hexadecanethiol SAMs. Semiautomated data analysis and a statistical model were developed to quantify cyclic deprotonation/protonation reactions on multiple arrays. In-plane force titrations were found to have the sensitivity to detect ionic hydrogen bond formation between protonated and nonprotonated carboxylic acid groups in the proximity of the surface pK1/2, which generated a mean tensile differential surface stress of +1.2 +/- 0.3 mN/m at pH 6.0, corresponding to 1 pN attractive force between two adjacent MHA molecules. Conversely, the magnitude of compressive differential surface stress was found to increase progressively with pH >/= 7.0, reaching a maximum of -14.5 +/- 0.5 mN/m at pH 9.0, attributed to enhanced electrostatic repulsion between deprotonated carboxylic acid groups. However, striking differences were observed in the micromechanical responses to different ionic strength and ion species present in the aqueous environment, highlighting the critical role of counter- and co-ions on surface stress. Our findings provide fundamental insights into the molecular mechanisms of in-plane mechanochemistry, which may be exploited for biosensing and nanoactuation applications.

Organic Ammonium Carboxylates as Supramolecular Building Blocks: The Role of Ionic Hydrogen Bonding

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The Structures and Proton Transfer Barriers in Proton-bound Homodimers of Aromatic Molecular Bases: Implication of Zero-point Energies for the Proton-transfer Reaction

),Zero-point energyThis study examines the energetics and structures ofproton-bound complexes with an ionic hydrogen bond,which, in recent years, has attracted increasing attention dueto their biological implications. Hydrogen bonding, as animportant intermolecular chemical interaction, plays asignificant role in many of chemical and biological pheno-mena. Structures and dynamics, specifically concerningsolvation and chemical reactions, are strongly influenced byhydrogen bonding. Extensive studies, both experimental andtheoretical, have been performed in order to understandhydrogen bonding in molecular systems of biological signi-ficance, such as DNA base pairs.

Coexistence of one- and two-dimensional supramolecular assemblies of terephthalic acid on Pd(111) due to self-limiting deprotonation

The adsorption of terephthalic acid [C(6)H(4)(COOH)(2), TPA] on a Pd(111) surface has been investigated by means of scanning tunneling microscopy (STM), x-ray photoelectron spectroscopy, and near-edge x-ray absorption fine structure spectroscopy under ultrahigh vacuum conditions at room temperature. We find the coexistence of one- (1D) and two-dimensional (2D) molecular ordering. Our analysis indicates that the 1D phase consists of intact TPA chains stabilized by a dimerization of the self-complementary carboxyl groups, whereas in the 2D phase, consisting of deprotonated entities, the molecules form lateral ionic hydrogen bonds. The supramolecular growth dynamics and the resulting structures are explained by a self-limiting deprotonation process mediated by the catalytic activity of the Pd surface. Our models for the molecular ordering are supported by molecular mechanics calculations and a simulation of high resolution STM images.

Theoretical study of the ionic hydrogen bond in the isolated proton-bound dimer of cytosine

We report a theoretical study of the ionic hydrogen bonding in the isolated proton-bound cytosine dimer, particularly in view of proton transfer. The theoretical study was carried out by B3LYP density functional and MP2 calculations. This study predicted 41.2 kcal/mol for the dissociation energy of the proton-bound dimer. The calculation of the transition state revealed a low barrier of 1.6 kcal/mol as well as a high rate constant of 5.9 × 10 11 s −1 for the proton transfer within the ionic hydrogen bond [B3LYP/6-311+G(2d,p)]. The stabilization in the transition state may provide the low energy pathway for the proton transfer.

Tetrabutylammonium-Induced Coacervation in Vesicular Solutions of Alkyl Carboxylic Acids for the Extraction of Organic Compounds

The potential of the tetrabutylammonium-induced liquid-liquid-phase separation in alkyl carboxylic acid vesicular solutions for the extraction of organic compounds prior to liquid chromatography was examined for the first time. The behavior of the coacervates yielded from octanoic to oleic acids as a function of the pH and salts was investigated. The time required for phase separation depended on the length of the carboxylic acid alkyl chain and the experimental procedure (i.e., standing, sonication, centrifugation, stirring, etc.). Theoretical preconcentration factors were a function of both surfactant concentration and the length of the alkyl chain, and they greatly surpassed those obtained with other surfactant-mediated separations (e.g., surfactant-rich phases from dodecanesulfonic acid or Triton X-114). Parameters affecting the extraction efficiency were assessed. Analytes in a wide polarity/charge range, (e.g., PAHs, surfactants, chlorophenols, bisphenols, phthalates, herbicides, amines, dyes, and photographic developers) were extracted with high efficiencies on the basis of the different types of interactions that the vesicular coacervates can establish (i.e., hydrophobic and ionic interactions, hydrogen bonds, and formation of mixed aggregates). The coacervates were compatible with the chromatographic determination of analytes following UV or MS detection. Their suitability for working under real conditions was checked by applying them to the extraction of nonionic surfactants [alkylphenol ethoxylates (octyl and nonyl) and alcohol ethoxylates (C12-C16)] from raw and treated sewage and to river water samples. Analytes in the coacervate were separated and quantified by liquid chromatography-ion trap mass spectrometry. No cleanup steps were necessary. Recoveries of the target compounds in the environmental water samples ranged from 89 to 103%.

Organic Ammonium Carboxylates as Supramolecular Building Blocks: The Role of Ionic Hydrogen Bonding

Ion pairs and higher order aggregates of organic ammonium carboxylates have been recognized as important tools in supramolecular chemistry. The structures of these species are attributed to isotropic electrostatic interaction and hydrogen bonds between oppositely charged ions. This account describes the role of hydrogen bonding in the crystal structures of various organic ­ammonium carboxylates. The utility of these salts in the design of supramolecular assemblies such as organogels and higher order clusters in non-polar solutions is also demonstrated.