Hydrogen-bonding Characteristics Research Articles

Hydrogen bonds to Au atoms in coordinated gold clusters

It is well known that various transition elements can form M···H hydrogen bonds. However, for gold, there has been limited decisive experimental evidence of such attractive interactions. Herein we demonstrate an example of spectroscopically identified hydrogen bonding interaction of C–H units to Au atoms in divalent hexagold clusters ([Au6]2+) decorated by diphosphine ligands. X-ray crystallography reveals substantially short Au–H/Au–C distances to indicate the presence of attractive interactions involving unfunctionalized C–H moieties. Solution 1H and 13C NMR signals of the C–H units appear at considerably downfield regions, indicating the hydrogen-bond character of the interactions. The Au···H interactions are critically involved in the ligand-cluster interactions to affect the stability of the cluster framework. This work demonstrates the uniqueness and potential of partially oxidised Au cluster moieties to participate in non-covalent interaction with various organic functionalities, which would expand the scope of gold clusters.

Investigating mutation-specific biological activities of small molecules using quantitative structure-activity relationship for epidermal growth factor receptor in cancer

Epidermal Growth Factor Receptor (EGFR) is a potential drug target in cancer therapy. Missense mutations play major roles in influencing the protein function, leading to abnormal cell proliferation and tumorigenesis. A number of EGFR inhibitor molecules targeting ATP binding domain were developed for the past two decades. Unfortunately, they become inactive due to resistance caused by new mutations in patients, and previous studies have also reported noticeable differences in inhibitor binding to distinct known driver mutants as well. Hence, there is a high demand for identification of EGFR mutation-specific inhibitors. In our present study, we derived a set of anti-cancer compounds with biological activities against eight typical EGFR known driver mutations and developed quantitative structure-activity relationship (QSAR) models for each separately. The compounds are grouped based on their functional scaffolds, which enhanced the correlation between compound features and respective biological activities. The models for different mutants performed well with a correlation coefficient, (r) in the range of 0.72–0.91 on jack-knife test. Further, we analyzed the selected features in different models and observed that hydrogen bond and aromaticity-related features play important roles in predicting the biological activity of a compound. This analysis is complimented with docking studies, which showed the binding patterns and interactions of ligands with EGFR mutants that could influence their activities.

Crystal structure of N-(4-hy-droxy-benz-yl)acetone thio-semicarbazone.

The structure of the title compound, C11H15N3OS, shows the flexibility due to the methyl-ene group at the thio-amide N atom in the side chain, resulting in the mol-ecule being non-planar. The dihedral angle between the plane of the benzene ring and that defined by the atoms of the thio-semicarbazide arm is 79.847 (4)°. In the crystal, the donor-acceptor hydrogen-bond character of the -OH group dominates the inter-molecular associations, acting as a donor in an O-H⋯S hydrogen bond, as well as being a double acceptor in a centrosymmetric cyclic bridging N-H⋯O,O' inter-action [graph set R22(4)]. The result is a one-dimensional duplex chain structure, extending along [111]. The usual N-H⋯S hydrogen-bonding association common in thio-semicarbazone crystal structures is not observed.

Molecular dynamics models and thermodynamic characteristics of hydrogen bonds in 1,2-ethanediol

A correlation between the lifetimes of hydrogen bonds and the thermodynamic characteristics of their formation and breaking, and the experimental relaxation times of dielectric spectra and the energy characteristics of relaxation processes, is observed via molecular dynamics (MD) simulation of the rearranging of the network structure of 1,2-ethanediol. The MD torsional frequency of the transition of gauche conformer tGg′ at 224.1 cm−1 and the experimental frequency of the band maximum of torsional vibrations at 230 cm−1 in the infrared spectrum correlate with the oscillation frequency of molecules at 240 cm−1 inside clusters in the Dissado–Hill (DH) model. The MD and DH models indicate a predominantly parallel alignment of the electric dipole moments of conformers tGg′ in the three-dimensional network of hydrogen bonds of the liquid 1,2-ethanediol phase.

On the nature of physical properties of water

The paper has analyzed relationships between lengths of covalent and hydrogen bonds and characteristic distances between oxygen atoms in water and ice, and also density of water and its isobaric and isothermal compressibility on temperature and pressure. It is shown that regularities of changes in properties of water are determined by the features of covalent and hydrogen bonds and electrostatic repulsion between oxygen atoms.

Core-hole-induced dynamical effects in the x-ray emission spectrum of liquid methanol.

We compute the x-ray emission spectrum of liquid methanol, with the dynamical effects that result from the creation of the core hole included in a semiclassical way. Our method closely reproduces a fully quantum mechanical description of the dynamical effects for relevant one-dimensional models of the hydrogen-bonded methanol molecules. For the liquid, we find excellent agreement with the experimental spectrum, including the large isotope effect in the first split peak. The dynamical effects depend sensitively on the initial structure in terms of the local hydrogen-bonding (H-bonding) character: non-donor molecules contribute mainly to the high-energy peak while molecules with a strong donating H-bond contribute to the peak at lower energy. The spectrum thus reflects the initial structure mediated by the dynamical effects that are, however, seen to be crucial in order to reproduce the intensity distribution of the recently measured spectrum.

Weak Supramolecular Interactions Governing Parallel and Antiparallel DNA Quadruplexes: Insights from Large-Scale Quantum Mechanics Analysis of Experimentally Derived Models.

The topology and energetics of guanine (G) quadruplexes is governed by supramolecular interactions within their strands. In this work, an extensive quantum mechanical (QM) study has been performed to analyze supramolecular interactions that shape the stems of (4+0) parallel (P) and (2+2) antiparallel (AP) quadruplex systems. The large-scale (≈400 atoms) models of P and AP were constructed from high-quality experimental structures. The results provide evidence that each of the P and AP structures is shaped by a distinct network of supramolecular interactions. Analysis of electron topological characteristics of hydrogen bonds in P and AP systems indicates that the P model benefits from stronger intratetrad hydrogen bonding. For intertetrad stacking interactions, both noncovalent interaction plot and energy decomposition analysis approaches suggest that the stem of the P quadruplex benefits more from stacking than that of the AP stem; the difference in energetic stabilization for the two topologies is about 10 %. Stronger hydrogen-bonding and stacking interactions in the stem of the P quadruplex, relative to those in the AP system, can be an important indicator to explain the experimental observations that guanine-rich oligonucleotides tend to form all-parallel stems with an all-anti orientation of nucleobases. However, in addition to intrinsic stabilization, partial desolvation effects, which affect the energetics and dynamics of the G-quadruplex folding process, call for further investigations.

An Efficient Synthesis of 3-Phosphorylated Benzoxaboroles via the Pudovik Reaction

A simple, fast and efficient synthesis of 3-phosphorylated benzoxaboroles using the Pudovik reaction is reported. A number of diverse 3-(dialkoxyphosphoryl)-1-hydroxy-3H-2,1-benzoxaboroles were synthesised in 70–86% yield. Interesting hydrogen bond features were observed in the crystal lattice of the 5-chlorinated 3-bis(benzyl­oxy)phosphoryl derivative with both inter- and intramolecular C–H···O hydrogen bonds. Additionally, linear chains of intermolecular O–H···O hydrogen bonds were observed.

Solid-State 17 O NMR Reveals Hydrogen-Bonding Energetics: Not All Low-Barrier Hydrogen Bonds Are Strong.

While NMR and IR spectroscopic signatures and structural characteristics of low-barrier hydrogen bond (LBHB) formation are well documented in the literature, direct measurement of the LBHB energy is difficult. Here, we show that solid-state 17 O NMR spectroscopy can provide unique information about the energy required to break a LBHB. Our solid-state 17 O NMR data show that the HB enthalpy of the O⋅⋅⋅H⋅⋅⋅N LBHB formed in crystalline nicotinic acid is only 7.7±0.5 kcal mol-1 , suggesting that not all LBHBs are particularly strong.

Molecular Dynamics Study of Water Flow across Multiple Layers of Pristine, Oxidized, and Mixed Regions of Graphene Oxide.

A molecular dynamics graphene oxide model is used to shed light on commonly overlooked features of graphene oxide membranes. The model features both perpendicular and parallel water flow across multiple sheets of pristine and/or oxidized graphene to simulate "brick-and-mortar" microstructures. Additionally, regions of pristine/oxidized graphene overlap that have thus far been overlooked in the literature are explored. Differences in orientational and hydrogen-bonding features between adjacent layers of water in this mixed region are found to be even more prominent than differences between pristine and oxidized channels. This region also shows lateral water flow in equilibrium simulations and orthogonal flow in non-equilibrium simulations significantly greater than those in the oxidized region, suggesting it may play a non-negligible role in the mechanism of water flow across graphene oxide membranes.

Evaluation of Reflexology by "BIOCERAMIC Resonance" Operation producing Weak Force Field during Simultaneous Acupoint Stimulation of Urinary Bladder Point on Subject's Ear Resulting in Electric Current Change on Urinary Bladder reflex Point on Subject's Hands, and Related New Research Finding.

It was postulated in our previous publications that the meridian channels as conceived in Traditional Chinese Medicine (TCM) are various standing waves arising from harmonic rhythmic sound frequencies originating from the human heart beat. BIOCERAMIC is an artificial material able to produce a weak force field causing different biophysical and systemic health benefits, with the key characteristics of hydrogen bonds weakening and microcirculation enhancement. Since discovering that the effects of a BIOCERAMIC field can be transmitted via sound waves propagation, we then also developed a BIOCERAMIC Resonance device to produce weak force field throughout the body, and achieve resonance with the body's meridian channels to reinforce microcirculation. Since our previous research proved BIOCERAMIC can produces changes in ectodermal current levels, the present evaluation on reflexology is done by the application of Electric Current Detection (ECD) to the palmar surface of the hands matching correlative organs and glands loci to reflex points according to standard reflexology. The procedure will compare changes in the electrical current observed before and after a session of BIOCERAMIC Resonance treatment on the soles of the subjects' feet. We also conducted a procedure using corona discharge (Kirlian) photography of the hands to examine whether the coronal intensities could be affected by application of the BIOCERAMIC patch. Intensities are shown on the screen of a computer using special software that categorizes intensities into five zones. Under the continuous treatment of BIOCERAMIC Resonance on soles of the feet and simultaneous stimulation on the specific point on the surface of the ear representing the urinary bladder. The electrical current (Aji ampere) on the areas in the hands are decreased from the beginning of the experiment, but only the specific area on the surface of the ear representing the urinary bladder was exhibited increased of the electrical current (Aji ampere), with statistically significant difference (p<0.05). To the other study we evaluated the validity of reflexology and corona discharge (Kirlian) photography by applying BIOCERAMIC Resonance and small adhesive patches made from the BIOCERAMIC material. Significant differences were evident on four out of five different zones of the computerized images. Our findings suggest the existence of presupposed virtual channels or reflex points on the skin surface of the feet, hands, and ears that connect or somehow reflect back to specific internal organs, as mapped out on standard charts found in reflexology. Furthermore, the depicted corona intensities from five zones shown on a computer screen of corona discharge photography seem to indicate that the volunteer subjects are affected by the BIOCERAMIC patches. This study demonstrates the operation of the BIOCERAMIC Resonance device is able to produce weak force field through the body, which is objectively measurable and thereby scientifically integrating the concepts of reflexology, meridian channels and biofield therapy.

How strong are H-bonds at the fully hydroxylated silica surfaces? Insights from the B3LYP electron density topological analysis

The calculation through the supermolecular approach of the hydrogen bond strength EHB between silanol groups at the surface of an ample class of silica-based materials is hindered by the intrinsic difficulty to define the “H-bond free” reference system. We propose, for the first time, to evaluate EHB by adopting the literature empirical correlation relating the Bader local electronic kinetic energy density Gb computed at the H⋅⋅⋅O bond critical point with EHB. Remarkably, EHB for the hydroxylated surfaces of quartz polymorphs correlates with surface formation energy, showing that the surface EHB is responsible of the surface stability. A number of correlations between hydrogen bond features are established, with that between EHB and the enhanced infrared intensity associated to surface hydrogen bond formation, obeying the literature formula semi-quantitatively. The present results are quite general and can be extended to other inorganic surfaces where hydrogen bonds between surface sites are the dominant features.

Potential mesogens based on pyridine derivatives: The geometric structure, conformational properties and characteristics of intermolecular hydrogen bonds

Conformational properties of the main part (excluding OC3H7 radicals) of the p-n-propyloxybenzoic (A1) and p-n-propyloxycinnamic (A2) acids molecules (relating to mesomorphic compounds) as well as p-n-propyloxybenzoic acid pyridine ester (B1) and p-n-propyloxyphenylazopyridine (B2) molecules (relating to non-mesomorphic compounds) were studied by DFT(B3LYP)/cc-pVTZ method. It was shown that the main parts of A1 and A2 acids are rigid. The barrier to internal rotation of pyridine fragment in the B1 and B2 molecules depends on the nature of the bridging group. It was determined that all studied A1⋯B1, A2⋯B1 and A2⋯B2 complexes are characterized by a strong hydrogen bond. The binding energy of complexes (≈14 kcal/mol, with BSSE corrections, DFT(B97D)/6-311++G**) exceeds the energy per hydrogen bond in the corresponding acid dimers (≈10 kcal/mol). The structural non-rigidity of A⋯B complexes is mainly caused by possibility of OC3H7 radicals internal rotation and A and B molecules rotation about the (H)O⋯N line. The characteristics of intermolecular hydrogen bonds were determined by NBO-analysis. The obtained results indicate that examined complexes correspond to the basic requirements to mesogen molecular forms. The thermodynamic functions of the gas-phase complexation reactions (idealized model of the complexes formation in the condensed state) were calculated. Preliminary studies of mesogen–non-mesogen A1⋯B2 system by differential scanning calorimetry and polarizing optical microscopy, showed that it has mesomorphic properties.

A prevalent intraresidue hydrogen bond stabilizes proteins.

Current limitations in de novo protein structure prediction and design suggest an incomplete understanding of the interactions that govern protein folding. Here we demonstrate that previously unappreciated hydrogen bonds occur within proteins between the amide proton and carbonyl oxygen of the same residue. Quantum calculations, infrared spectroscopy, and nuclear magnetic resonance spectroscopy show that these interactions share hallmark features of canonical hydrogen bonds. Biophysical analyses demonstrate that selective attenuation or enhancement of these C5 hydrogen bonds affects the stability of synthetic β-sheets. These interactions are common, affecting approximately 5% of all residues and 94% of proteins, and their cumulative impact provides several kcal/mol of conformational stability to a typical protein. C5 hydrogen bonds stabilize, especially, the flat β-sheets of the amyloid state, which is linked with Alzheimer’s disease and other neurodegenerative disorders. Inclusion of these interactions in computational force fields would improve models of protein folding, function, and dysfunction.

Multi-centred hydrogen bonds between water and perchlorate anion

ABSTRACTResults of classical molecular dynamics simulations are presented for the re-orientational dynamics of water hydrogen bonded to perchlorate anion. Different mechanisms of bond formation are presented. Due to its regular tetrahedron geometry the perchlorate anion can make classical as well as bifurcated and trifurcated hydrogen bonds. The angular variation of water in the first solvation shell of perchlorate suggests the transitional character of multi-centred hydrogen bonds. As a result water molecules can slide around the anion.

Sensing Activity of a New Generation of Thiourea-based Receptors; A Theoretical Study on the Anion Sensing

A theoretical density functional theory (DFT) study was performed on a series of the neutral N-phenylthiourea substituents (p-OC2H5, p-CH3, m-CH3, H, p-Cl, p-Br, m-Cl, and p-NO2) as the sensor of acetate and fluoride anions. The hydrogen bond character was analyzed as a scale of the sensing activity. It was confirmed that hydrogen bond between the p-NO2 derivatives of N-phenylthiourea and fluoride anion is stronger than acetate in CH3CN as a solvent. Therefore, N-(p-nitrophenyl) thiourea acts as a better chemical sensor in fluoride detection. For the investigation of the N-H bond properties, donor-acceptor interaction energy through the natural bond orbital analysis was obtained. Topology analysis by estimation of the kinetic and potential energy densities of the hydrogen bonds was done. Finally, some correlations between the quantum chemistry descriptors and sensing characters of the studied compounds were obtained and analyzed.

Time-dependent density functional theory study on the excited-state hydrogen-bonding characteristics of polyaniline in aqueous environment

A theoretical study was carried out to study the excited-state of hydrogen-bonding characteristics of polyaniline (PANI) in aqueous environment. The hydrogen-bonded PANI-H2O complexes were studied using first-principles calculations based on density functional theory (DFT). The electronic excitation energies and the corresponding oscillator strengths of the low-lying electronically excited states for hydrogen-bonded complexes were calculated by time-dependent density functional theory (TDDFT). The ground-state geometric structures were optimized, and it is observed that the intermolecular hydrogen bonds CN⋯HO and NH⋯OH were formed in PANI-H2O complexes. The formed hydrogen bonds influenced the bond lengths, the charge distribution, as well as the spectral characters of the groups involved. It was concluded that all the hydrogen-bonded PANI-H2O complexes were primarily excited to the S1 states with the largest oscillator strength. In addition, the orbital transition from the highest occupied molecular orbital (HOMO) to the lowest unoccupied molecular orbital (LUMO) involved intramolecular charge redistribution resulting to increase the electron density of the quinonoid rings.

Hydrogen-bonding characteristics and unique ring-opening polymerization behavior ofOrtho-methylol functional benzoxazine

Monofunctional benzoxazine with ortho-methylol functionality has been synthesized and highly purified. The chemical structure of the synthesized monomer has been confirmed by 1H and 13C nuclear magnetic resonance spectroscopy (NMR), Fourier transform infrared spectroscopy (FT-IR) and elemental analysis. One-dimensional (1D) 1H NMR is used with respect to varied concentration of benzoxazines to study the specific nature of hydrogen bonding in both ortho-methylol functional benzoxazine and its para counterpart. The polymerization behavior of benzoxazine monomer has been also studied by in situ FT-IR and differential scanning calorimetry, experimentally supporting the polymerization mechanism of ortho-methylol functional benzoxazine we proposed before. © 2016 Wiley Periodicals, Inc. J. Polym. Sci., Part A: Polym. Chem. 2016, 54, 3635–3642

Activity coefficients at infinite dilution for organic solutes dissolved in two 1,2,3-tris(diethylamino)cyclopenylium based room temperature ionic liquids

Infinite dilution activity coefficients and gas-to-liquid partition coefficients have been determined for at least 45 different organic solutes of varying polarity and hydrogen-bonding character dissolved in anhydrous 1,2,3-tris(diethylamino)cyclopropenylium dicyanamide, ([TDC]+[DCA]−), and 1,2,3-tris(diethylamino)cyclopropenylium bis(trifluoromethylsulfonyl)imide, ([TDC]+[Tf2N]−). The measured infinite dilution activity coefficients were used to calculation selectivity values for various practical separation problems. Computations showed ([TDC]+[DCA]−) should afford better performance in hexane/benzene and hexane/pyridine separation problems than sulfolane and N-methyl-2-pyrrolidone. Abraham model correlations were derived for predicting solute transfer into both ([TDC]+[DCA]−) and ([TDC]+[Tf2N]−) from water and from the gas phase. The derived correlations describe the observed solute transfer partition coefficients to within 0.13 (or fewer) log units.

Hydrogen bond lifetimes in supercritical methanol–water mixtures via MD simulation

ABSTRACTDynamical features of hydrogen bonds in methanol–water mixtures have been analysed in terms of lifetime in the wide range of conditions, including supercritical states, using a molecular dynamics simulation with flexible potential models. Hydrogen bond characteristics in methanol–water mixtures were investigated by considering the combination of molecular species and donor–acceptor of hydrogen-bonded molecules. The hydrogen bond lifetimes mainly depend on temperature, and those in supercritical condition were about 1/10th of that at ambient condition. Focusing on the composition dependence of the hydrogen bond lifetime, the unique behaviour of that resulting from hydration structure was observed. Moreover, the molecular combination, which showed the largest hydrogen bond lifetime, was different for ambient and high temperature and high pressure conditions. The relationship between hydrogen bond lifetime and molar volume was also calculated to discuss the hydrogen bond lifetime in terms of the collision frequency of molecules and the intermolecular distance.