Showing papers on "Hydrogen bond published in 2018"

Electrostatic Interactions in Protein Structure, Folding, Binding, and Condensation

Abstract: Charged and polar groups, through forming ion pairs, hydrogen bonds, and other less specific electrostatic interactions, impart important properties to proteins. Modulation of the charges on the amino acids, e.g., by pH and by phosphorylation and dephosphorylation, have significant effects such as protein denaturation and switch-like response of signal transduction networks. This review aims to present a unifying theme among the various effects of protein charges and polar groups. Simple models will be used to illustrate basic ideas about electrostatic interactions in proteins, and these ideas in turn will be used to elucidate the roles of electrostatic interactions in protein structure, folding, binding, condensation, and related biological functions. In particular, we will examine how charged side chains are spatially distributed in various types of proteins and how electrostatic interactions affect thermodynamic and kinetic properties of proteins. Our hope is to capture both important historical developments and recent experimental and theoretical advances in quantifying electrostatic contributions of proteins.

Enhanced Adsorption of p-Arsanilic Acid from Water by Amine-Modified UiO-67 as Examined Using Extended X-ray Absorption Fine Structure, X-ray Photoelectron Spectroscopy, and Density Functional Theory Calculations.

Abstract: p-Arsanilic acid (p-ASA) is an emerging organoarsenic pollutant comprising both inorganic and organic moieties For the efficient removal of p-ASA, adsorbents with high adsorption affinity are urgently needed Herein, amine-modified UiO-67 (UiO-67-NH2) metal–organic frameworks (MOFs) were synthesized, and their adsorption affinities toward p-ASA were 2 times higher than that of the pristine UiO-67 Extended X-ray absorption fine structure (EXAFS), X-ray photoelectron spectroscopy (XPS), and density functional theory (DFT) calculation results revealed adsorption through a combination of As–O–Zr coordination, hydrogen bonding, and π–π stacking, among which As–O–Zr coordination was the dominant force Amine groups played a significant role in enhancing the adsorption affinity through strengthening the As–O–Zr coordination and π–π stacking, as well as forming new adsorption sites via hydrogen bonding UiO-67-NH2s could remove p-ASA at low concentrations (<5 mg L–1) in simulated natural and wastewaters to an a

Conjugated Energetic Salts Based on Fused Rings: Insensitive and Highly Dense Materials.

Abstract: Nitroamino-functionalized 1,2,4-triazolo[4,3-b][1,2,4,5]tetrazine (1), when combined with intermolecular hydrogen bonds (HBs) and strong noncovalent interactions between layers, results, for example, in an interlayer distance of 2.9 A for dihydroxylammonium 3,6-dinitramino-1,2,4-triazolo[4,3-b][1,2,4,5]tetrazine (2c) with a packing coefficient of 0.805. For dihydroxylammonium 6,6′-dinitramino-3,3′-azo-1,2,4-triazolo[4,3-b][1,2,4,5]tetrazine (3b), two fused rings are linked by an azo group, which expands the conjugated system resulting in an even shorter interlayer distance of 2.7 A and a higher packing coefficient of 0.807. These values appear to be the shortest interlayer distances and the highest packing coefficients reported for tetrazine energetic materials. With high packing coefficients, both possess high densities of 1.92 g cm–3 and 1.99 g cm–3 at 293 K, respectively. Compared with its precursor, the hydroxylammonium moiety serves as a buffer chain (H–N–O–H), connecting the anion and cation through...

Electrochemical-Oxidation-Induced Site-Selective Intramolecular C(sp3)–H Amination

Abstract: The cross-coupling of C(sp3)–H and N–H represents one of the most straightforward approaches to construct saturated nitrogen-containing compounds The additional oxidants or halogenated reagents are generally required in such processes Herein, we developed an electrochemical oxidative intramolecular C(sp3)–H amination of amides by employing a carbon rod anode and a platinum plate cathode in an undivided cell under constant-current electrolysis conditions Tetrabutylammonium acetate was not only employed as an electrolyte, but also can form the intermolecular hydrogen bond with amide and promote cleavage of the N–H bond The additional oxidants and N-halogenation step can be obviated in this methodology A variety of benzylic and nonactivated tertiary, secondary, primary C(sp3)–H amination can be achieved with good yields

Intriguing role of water in protein-ligand binding studied by neutron crystallography on trypsin complexes.

Abstract: Hydrogen bonds are key interactions determining protein-ligand binding affinity and therefore fundamental to any biological process. Unfortunately, explicit structural information about hydrogen positions and thus H-bonds in protein-ligand complexes is extremely rare and similarly the important role of water during binding remains poorly understood. Here, we report on neutron structures of trypsin determined at very high resolutions ≤1.5 A in uncomplexed and inhibited state complemented by X-ray and thermodynamic data and computer simulations. Our structures show the precise geometry of H-bonds between protein and the inhibitors N-amidinopiperidine and benzamidine along with the dynamics of the residual solvation pattern. Prior to binding, the ligand-free binding pocket is occupied by water molecules characterized by a paucity of H-bonds and high mobility resulting in an imperfect hydration of the critical residue Asp189. This phenomenon likely constitutes a key factor fueling ligand binding via water displacement and helps improving our current view on water influencing protein–ligand recognition.

NiCu single atom alloys catalyze the CH bond activation in the selective non- oxidative ethanol dehydrogenation reaction

Abstract: NiCu single atom alloy (SAA) nanoparticles supported on silica are reported to catalyze the non-oxidative dehydrogenation of ethanol, selectively to acetaldehyde and hydrogen products by facilitating the C H bond cleavage. The activity and selectivity of the NiCu SAA catalysts were compared to monometallic copper and to PtCu and PdCu single atom alloys, in a flow reactor at moderate temperatures. In-situ DRIFTS showed that the silica support facilitates the O H bond cleavage of ethanol to form ethoxy intermediates over all the supported alloy catalysts. However, these remain unreactive up to 250 °C for the Cu/SiO2 monometallic nanoparticles, while in the NiCu SAA, acetaldehyde is formed at much lower temperatures, below 150 °C. In situ DRIFTS was also used to identify the C H activation step as the rate determining step of this reaction on all the copper catalysts we examined. The presence of atomically dispersed Ni in Cu significantly lowers the C H bond activation barrier, whereas Pt and Pd atoms were found less effective. This work provides direct evidence that the C H bond cleavage is the rate determining step in ethanol dehydrogenation over this type catalyst.

Influence of Hydration on the Structure of Reline Deep Eutectic Solvent: A Molecular Dynamics Study.

Abstract: In this article, we have performed an all-atom molecular dynamics simulation study to investigate the influence of water on the molecular level arrangement of reline deep eutectic solvent for different hydration levels ranging from 3.4 to 58.1 wt % of water and complemented the observations of recently measured neutron scattering experimental data. This study is particularly important because water is being introduced as a second hydrogen bond donor/acceptor in reline, wherein the structure is primarily governed by hydrogen bonding and electrostatic interactions. We have analyzed the simulated X-ray scattering structure functions, their partial components, and hydrogen bonding interactions to understand the effects of water on various intermolecular interactions in reline–water mixtures. It is observed that at lower hydration level, reline structure is qualitatively retained. At higher hydration level, most water molecules preferentially solvate chloride anions and ammonium group of choline cations mostly...

QM/MM studies into the H2O2-dependent activity of lytic polysaccharide monooxygenases: evidence for the formation of a caged hydroxyl radical intermediate

Abstract: Lytic polysaccharide monooxygenases (LPMOs) are promising enzymes for the conversion of lignocellulosic biomass into biofuels and biomaterials. Classically considered oxygenases, recent work suggests that H2O2 can, under certain circumstances, also be a potential substrate. Here we present a detailed mechanism of the activation of H2O2 by a C4-acting LPMO using small-model DFT and QM/MM calculations. We show that there is an efficient mechanism to break the O–O bond of H2O2, with a low barrier of 5.8 kcal/mol, via a one-electron transfer from the LPMO-Cu(I) site to form an HO• radical, stabilized by hydrogen bonding interactions. Our QM/MM calculations further show that the H-bonding machinery of the enzyme directs the HO• radical to abstract a hydrogen atom from the Cu(II)–OH unit rather than from the substrate in what is essentially a caged-radical reaction, thereby forming a Cu(II)-oxyl species. The Cu(II)-oxyl species then exclusively oxidizes the C4–H bond due to the suitable position of the substrat...

Molecular Recognition of Hydrophilic Molecules in Water by Combining the Hydrophobic Effect with Hydrogen Bonding.

Abstract: During the last half a century, great achievements have been made in molecular recognition in parallel with the invention of numerous synthetic receptors. However, the selective recognition of hydrophilic molecules in water remains a generally accepted challenge in supramolecular chemistry but is commonplace in nature. In an earlier Communication [Huang et al. J. Am. Chem. Soc. 2016, 138, 14550], we reported a pair of endo-functionalized molecular tubes that surprisingly prefer highly hydrophilic molecules over hydrophobic molecules of a similar size and shape. The hydrophobic effect and hydrogen bonding were proposed to be responsible, but their exact roles were not fully elucidated. In this Article, we present a thorough study on the binding behavior of these molecular tubes toward 44 hydrophilic molecules in water. Principal component analysis reveals that the binding strength is weakly correlated to the hydrophobicity, volume, surface area, and dipole moment of guests. Furthermore, molecular dynamics ...

A Thiourea Tether in the Second Coordination Sphere as a Binding Site for CO2 and a Proton Donor Promotes the Electrochemical Reduction of CO2 to CO Catalyzed by a Rhenium Bipyridine-Type Complex.

Abstract: The electrochemical reduction of CO2 has been extensively investigated in recent years, with the expectation that a detailed mechanistic understanding could achieve the goal of finding a stable catalyst with high turnover frequencies and low reduction potentials. In the catalytic cycle of the carbon dioxide hydrogenase enzyme, it has been suggested that the reduced metal center reacts with CO2 to form a carboxylate intermediate that is stabilized by hydrogen bonding using a histidine moiety in the second coordination sphere. Using the well-known fac-Re(I)bipyridine(CO)3Cl complex as a starting point, the bipyridine ligand was modified in the second coordination sphere with a thiourea tether that is known to form hydrogen bonds with carbonyl moieties. The resulting Re(I) catalyst was an excellent electrocatalyst for the selective reduction of CO2 to CO, with a turnover frequency of 3040 s–1. The binding of CO2 to the thiourea tether was observable by 1H NMR, and NOE experiments showed that the hydrogen ato...

On the molecular origin of the cooperative coil-to-globule transition of poly(N-isopropylacrylamide) in water

Abstract: By means of atomistic molecular dynamics simulations we investigate the behaviour of poly(N-isopropylacrylamide), PNIPAM, in water at temperatures below and above the lower critical solution temperature (LCST), including the undercooled regime. The transition between water soluble and insoluble states at the LCST is described as a cooperative process involving an intramolecular coil-to-globule transition preceding the aggregation of chains and the polymer precipitation. In this work we investigate the molecular origin of such cooperativity and the evolution of the hydration pattern in the undercooled polymer solution. The solution behaviour of an atactic 30-mer at high dilution is studied in the temperature interval from 243 to 323 K with a favourable comparison to available experimental data. In the water soluble states of PNIPAM we detect a correlation between polymer segmental dynamics and diffusion motion of bound water, occurring with the same activation energy. Simulation results show that below the coil-to-globule transition temperature PNIPAM is surrounded by a network of hydrogen bonded water molecules and that the cooperativity arises from the structuring of water clusters in proximity to hydrophobic groups. Differently, the perturbation of the hydrogen bond pattern involving water and amide groups occurs above the transition temperature. Altogether these findings reveal that even above the LCST PNIPAM remains largely hydrated and that the coil-to-globule transition is related with a significant rearrangement of the solvent in the proximity of the surface of the polymer. The comparison between the hydrogen bonding of water in the surrounding of PNIPAM isopropyl groups and in the bulk displays a decreased structuring of solvent at the hydrophobic polymer–water interface across the transition temperature, as expected because of the topological extension along the chain of such interface. No evidence of an upper critical solution temperature behaviour, postulated in theoretical and thermodynamics studies of PNIPAM aqueous solution, is observed in the low temperature domain.

Chiral Magnesium Bisphosphate Catalyzed Asymmetric Double C(sp3)–H Bond Functionalization Based on Sequential Hydride Shift/Cyclization Process

Abstract: Described herein is a chiral magnesium bisphosphate-catalyzed asymmetric double C(sp3)–H bond functionalization triggered by a sequential hydride shift/cyclization process. This reaction consists of stereoselective domino C(sp3)–H bond functionalization: (1) a highly enantio- and diastereoselective C(sp3)–H bond functionalization by chiral magnesium bisphosphate (first [1,5]-hydride shift), and (2) a highly diastereoselective C(sp3)–H bond functionalization by an achiral catalyst (Yb(OTf)3, second [1,5]-hydride shift).

Hydrophobic Hydration and the Effect of NaCl Salt in the Adsorption of Hydrocarbons and Surfactants on Clathrate Hydrates.

Abstract: Adsorption of functional molecules on the surface of hydrates is key in the understanding of hydrate inhibitors. We investigate the adsorption of a hydrocarbon chain, nonionic and ionic surfactants, and ions at the hydrate–aqueous interface. Our results suggest a strong connection between the water ordering around solutes in bulk and the affinity for the hydrates surface. We distinguish two types of water ordering around solutes: (i) hydrophobic hydration where water molecules form a hydrogen bond network similar to clathrate hydrates, and (ii) ionic hydration where water molecules align according to the polarity of an ionic group. The nonionic surfactant and the hydrocarbon chain induce hydrophobic hydration and are favorably adsorbed on the hydrate surface. Adsorption of ions and the ionic headgroups on the hydrate surface is not favorable because ionic hydration and the hydrogen bond structure of hydrates are incompatible. The nonionic surfactant is adsorbed by the headgroup and tail while adsorption o...

A theoretical study of the effect of a non-aqueous proton donor on electrochemical ammonia synthesis

Abstract: Ammonia synthesis is one of the most studied reactions in heterogeneous catalysis. To date, however, electrochemical N2 reduction in aqueous systems has proven to be extremely difficult, mainly due to the competing hydrogen evolution reaction (HER). Recently, it has been shown that transition metal complexes based on molybdenum can reduce N2 to ammonia at room temperature and ambient pressure in a non-aqueous system, with a relatively small amount of hydrogen output. We demonstrate that the non-aqueous proton donor they have chosen, 2,6-lutidinium (LutH+), is a viable substitute for hydronium in the electrochemical process at a solid surface, since this donor can suppress the HER rate. We also show that the presence of LutH+ can selectively stabilize the *NNH intermediate relative to *NH or *NH2via the formation of hydrogen bonds, indicating that the use of non-aqueous solvents can break the scaling relationship between limiting potential and binding energies.

Facile Synthesis of Self-Assembled g-C3N4 with Abundant Nitrogen Defects for Photocatalytic Hydrogen Evolution

Abstract: In this work, g-C3N4 with different morphologies is prepared using melamine as precursor via self-assembly and calcination. Compared with pristine g-C3N4, the resultant materials possess thinner lamellar structure and abundant nitrogen defects. Hydrolysis of partial melamine occurs in a hydrothermal process, and a consequent supramolecular intermediate is formed between melamine and its hydrolysates via hydrogen bonding. In addition to enlarging the π–π conjugated systems of the polymer, the formation of intermolecular hydrogen bonds is also interesting for increasing the lifetime of fluorescence as well as for decreasing the recombination rate of electron–hole pairs. Optical absorption characterization indicates that the samples formed by surface self-assembly show remarkably extended light absorption in the visible-light region in comparison with the original g-C3N4. Under visible-light irradiation, all modified materials have outstanding photocatalytic activity, especially the optimally modified cataly...

Acid···Amide Supramolecular Synthon in Cocrystals: From Spectroscopic Detection to Property Engineering

Abstract: The acid···amide dimer heterosynthon in cocrystals of aromatic acids and primary amides is identified by marker peaks in the IR spectra that are characteristic of individual N–H···O and O–H···O interactions and also of the extended synthon. The O–H···O hydrogen bond is crucial to heterodimer formation in contrast to the N–H···O bond. A combinatorial study, tuning the chemical nature of acid and amide functionalities, leads to 22 cocrystals out of 36 crystallization attempts. Four quadrants I–IV are defined based on acidity and basicity of the acid and amide components. The strong acid–strong base combination in quadrant I favors the planar acid···amide heterodimer in its eight cocrystals. Quadrant IV with its weak acid–weak base combination is the least favored for the planar heterosynthon and synthon diversity is observed in the eight cocrystals obtained. The strong–weak and weak–strong combinations in quadrants II and III are expectedly ambivalent. This exercise highlights the effect of molecular featur...

Noncovalent Carbon-Bonding Interactions in Proteins

Abstract: Carbon bonds (C-bonds) are the highly directional noncovalent interactions between carbonyl-oxygen acceptors and sp3 -hybridized-carbon σ-hole donors through n→σ* electron delocalization. We have shown the ubiquitous existence of C-bonds in proteins with the help of careful protein structure analysis and quantum calculations, and have precisely determined C-bond energies. The importance of conventional noncovalent interactions such as hydrogen bond (H-bonds) and halogen bond (X-bonds) in the structure and function of biological molecules are well established, while carbon bonds C-bonds have still to be recognized. We have shown that C-bonds are present in proteins, contribute enthalpically to the overall hydrophobic interaction and play a significant role in the photodissociation mechanism of myoglobin and the binding of nucleobases to proteins.

σ-Holes and σ-lumps direct the Lewis basic and acidic interactions of noble metal nanoparticles: introducing regium bonds.

Abstract: Using local DFT-based probes for electrostatic as well as charge transfer/polarization interactions, we are able to characterize Lewis basic and acidic sites on copper, silver and gold nanoparticles. The predictions obtained using the DFT-probes are compared to the interaction energies of the electron donating (CO, H2O, NH3 and H2S) and the electron accepting (BH3, BF3, HCl [H-down] and Na+) compounds. The probes include the local electron attachment energy [E(r)], the average local ionization energy [Ī(r)], and the electrostatic potential [V(r)] and are evaluated on isodensity surfaces located at distances corresponding to typical interaction distances. These probes have previously been successful in characterizing molecular interactions. Good correlations are found between Lewis acidity and maxima in V(r), appearing as a consequence of σ-holes, as well as minima in E(r), of the noble metal nanoparticles. Similarly are Lewis basic sites successfully described by surface minima in V(r) and Ī(r); the former are indicative of σ-lumps, i.e. regions of enhanced σ-density. The investigated probes are anticipated to function as reliable tools in nanoparticle reactivity and interaction characterization, and may act as suitable descriptors in large-scale screenings for materials of specific properties, e.g. in heterogeneous catalysis. Because of the similarity between the noble metal nanoparticle's interactions with Lewis bases and the concepts of halogen and hydrogen bonding, a new class of bonds is introduced – regium bonds – taking place between a σ-hole of a Cu, Ag or Au compound and an electron donor.

Amide-Containing Alkyl Chains in Conjugated Polymers: Effect on Self-Assembly and Electronic Properties

Abstract: A simple and efficient strategy to modulate the self-assembly and solid-state morphology of conjugated polymers has been developed by incorporating various amounts of amide-containing alkyl side chains to high charge carrier mobility conjugated polymers based on diketopyrrolopyrrole (DPP) Synthetically easily accessible and tunable, the incorporation of amide-containing side chains is a direct strategy to promote intermolecular hydrogen bonding between polymer chains and tune the solid-state morphology Incorporation of 5–30 mol % of amides in the conjugated polymers was performed without a drastic decrease of solubility The incorporation of hydrogen-bonding moieties allowed for an improvement of the charge carrier mobility in organic field-effect transistors (OFET) devices, which achieved a maximum value of 246 cm2/(V s) at 5 mol % of amides Morphological investigation showed that the intermolecular hydrogen bonds formed between adjacent amide moieties directly affected the lamellar packing of the po

Rational Design of Mononuclear Iron Porphyrins for Facile and Selective 4e–/4H+ O2 Reduction: Activation of O–O Bond by 2nd Sphere Hydrogen Bonding

Abstract: Facile and selective 4e–/4H+ electrochemical reduction of O2 to H2O in aqueous medium has been a sought-after goal for several decades Elegant but synthetically demanding cytochrome c oxidase mimics have demonstrated selective 4e–/4H+ electrochemical O2 reduction to H2O is possible with rate constants as fast as 105 M–1 s–1 under heterogeneous conditions in aqueous media Over the past few years, in situ mechanistic investigations on iron porphyrin complexes adsorbed on electrodes have revealed that the rate and selectivity of this multielectron and multiproton process is governed by the reactivity of a ferric hydroperoxide intermediate The barrier of O—O bond cleavage determines the overall rate of O2 reduction and the site of protonation determines the selectivity In this report, a series of mononuclear iron porphyrin complexes are rationally designed to achieve efficient O—O bond activation and site-selective proton transfer to effect facile and selective electrochemical reduction of O2 to water In

Oxygen Reduction Reaction Promoted by Manganese Porphyrins

Abstract: The oxygen reduction reaction (ORR) is catalyzed by manganese(II) porphyrins in the presence of Bronsted acids (HAs). Analyses of the catalytic cyclic voltammetric profiles have permitted the ORR mechanism to be constructed and rate constants to be extracted for both the formation of the initial oxygen adduct and the O–O bond cleavage event for a series of HAs. The dependence of the formation rate constant of the oxygen adduct on reactant concentrations reveals a rate law that is first order in Mn porphyrin and oxygen substrate. A second order dependence in HA is observed for unadorned Mn porphyrin platforms whereas with Mn hangman porphyrin, a proton is provided intramolecular to the oxygen adduct and consequently the HA order is reduced to unity. The stabilization of the oxygen adduct with an additional hydrogen bond from HA engenders a rate-determining step involving O–O bond cleavage, resulting in the rare instance where the activation of the O–O bond is directly observed.

Dissecting Porosity in Molecular Crystals: Influence of Geometry, Hydrogen Bonding, and [π···π] Stacking on the Solid-State Packing of Fluorinated Aromatics

Abstract: Porous molecular crystals are an emerging class of porous materials that is unique in being built from discrete molecules rather than being polymeric in nature. In this study, we examined the effects of molecular structure of the precursors on the formation of porous solid-state structures with a series of 16 rigid aromatics. The majority of these precursors possess pyrazole groups capable of hydrogen bonding, as well as electron-rich aromatics and electron-poor tetrafluorobenzene rings. These precursors were prepared using a combination of Pd- and Cu-catalyzed cross-couplings, careful manipulations of protecting groups on the nitrogen atoms, and solvothermal syntheses. Our study varied the geometry and dimensions of precursors, as well as the presence of groups capable of hydrogen bonding and [π···π] stacking. Thirteen derivatives were crystallographically characterized, and four of them were found to be porous with surface areas between 283 and 1821 m2 g–1. Common to these four porous structures were (a...