Asymmetric Hydrogen Bond Research Articles

Synthesis and crystal structure of (NH4)[Ni3(HAsO4)(AsO4)(OH)2

The title compound, ammonium trinickel(II) hydrogen arsenate arsenate di-hydroxide, was synthesized under hydro-thermal conditions. Its crystal structure is isotypic with that of K[Cu3(HAsO4)(AsO4)(OH)2] and is characterized by pseudo-hexa-gonal (001) 2 ∞[Ni3As2O18/3(OH)6/3O1/1(OH)1/1]- layers formed from vertex- and edge-sharing [NiO4(OH)2] octa-hedra and [AsO3.5(OH)0.5] tetra-hedra as the building units. The hydrogen atom of the OH group shows occupational disorder and was refined with a site occupation factor of 1/2, indicating the equal presence of [HAsO4]2- and [AsO4]3- groups. Strong asymmetric hydrogen bonds between symmetry-related (O,OH) groups of the arsenate units [O⋯O = 2.588 (18) Å] as well as hydrogen bonds accepted by these (O,OH) groups from OH groups bonded to the NiII atoms [O⋯O = 2.848 (12) Å] link adjacent layers. Additional consolidation of the packing is achieved through N-H⋯O hydrogen bonds from the ammonium ion, which is sandwiched between adjacent layers [N⋯O = 2.930 (7) Å] although the H atoms could not be located in the present study. The presence of the pseudo-hexa-gonal 2 ∞[Ni3As2O18/3(OH)6/3O1/1(OH)1/1]- layers may be the reason for the systematic threefold twinning of (NH4)[Ni3(HAsO4)(AsO4)(OH)2] crystals. Significant overlaps of the reflections of the respective twin domains complicated the structure solution and refinement.

Chalcogen bonding catalysis.

Catalysts play a major role in chemical synthesis, and catalysis is considered to be a green and economic process. Catalysis is dominated by covalent interactions between the catalyst and substrate. The design of non-covalent catalysts came into limelight only recently. Hydrogen bonding (HB) catalysts are well established among non-covalent catalysts, including asymmetric HB catalysts. Though halogen bonding (XB) catalysis and its asymmetric version are gaining admiration, non-covalent chalcogen bonding catalysis (ChB) is in the budding stage. This tutorial review will focus on the recently evolved chalcogen bonding catalysis and emphasis will be given to the chalcogen bonding of chiral molecules. Since successful enantioselective chalcogen bonding catalysis is yet to be reported, this review will focus on the basics of non-covalent bonding catalysis, chalcogen bonding catalysis, chiral chalcogenide synthesis, rigidification of transition states by ChB, stabilization of cations by chiral chalcogens, details of unsuccessful asymmetric chalcogen bonding catalysis, enantioseparation of racemic molecules using ChB, and the existence of ChB in chiral biomolecules.

Chirality-Dependent Structural Transformation in Chiral 2D Perovskites under High Pressure.

Chiral perovskites have attracted considerable attention owing to their potential applications in spintronic- and polarization-based optoelectronic devices. However, the structural chirality/asymmetry transfer mechanism between chiral organic ammoniums and achiral inorganic frameworks is still equivocal, especially under extreme conditions, as the systematic structural differences between chiral and achiral perovskites have been rarely explored. Herein, we successfully synthesized a pair of new enantiomeric chiral perovskite (S/R-3PYEA)PbI4 (3PYEA2+ = C5NH5C2H4NH32+) and an achiral perovskite (rac-3PYEA)PbI4. Hydrostatic pressure was used, for the first time, to systematically investigate the differences in the structural evolution and optical behavior between (S/R-3PYEA)PbI4 and (rac-3PYEA)PbI4. At approximately 7.0 GPa, (S/R-3PYEA)PbI4 exhibits a chirality-dependent structural transformation with a bandgap "red jump" and dramatic piezochromism from translucent red to opaque black. Upon further compression, a previously unreported chirality-induced negative linear compressibility (NLC) is achieved in (S/R-3PYEA)PbI4. High-pressure structural characterizations and first-principles calculations demonstrate that pressure-driven homodirectional tilting of homochiral ammonium cations strengthens the interactions between S/R-3PYEA2+ and Pb-I frameworks, inducing the formation of new asymmetric hydrogen bonds N-H···I-Pb in (S/R-3PYEA)PbI4. The enhanced asymmetric H-bonding interactions further break the symmetry of (S/R-3PYEA)PbI4 and trigger a greater degree of in-plane and out-of-plane distortion of [PbI6]4- octahedra, which are responsible for chirality-dependent structural phase transition and NLC, respectively. Nevertheless, the balanced H-bonds incurred by equal proportions of S-3PYEA2+ and R-3PYEA2+ counteract the tilting force, leading to the absence of chirality-dependent structural transition, spectral "red jump", and NLC in (rac-3PYEA)PbI4.

A crystal structure refinement of uralolite, Ca2Be4(PO4)3(OH)3∙5H2O, from Weinebene, Austria

The crystal structure of uralolite, Ca2Be4(PO4)3(OH)3·5H2O, from the spodumene deposit of Weinebene, Carinthia, Austria, has been refined with X-ray single crystal data gathered on a CCD diffractometer. Uralolite is monoclinic, space group P21/n, a = 6.553(1), b = 16.005(3), c = 15.979(3) Å, β = 101.63(1)°, V = 1641.5(5) Å3. While previously only isotropic displacement parameters and no hydrogen atom positions were reported for uralolite, now anisotropic displacement parameters were used for non-hydrogen atoms and hydrogen atoms were located and refined yielding R1 = 0.038 for 3909 observed reflections. Uralolite is built up from corrugated layers [Be4(PO4)3(OH)3]4- parallel to (010), which contain Z-shaped groups of four BeO4 tetrahedra sharing corners via three OH groups and are further crosslinked by PO4 tetrahedra. Two Ca atoms in Ca(Ophosphate)5(H2O)2 coordination and an interstitial water molecule link these layers along [010]. The OH groups and the Ca-bonded H2O molecules are all involved in hydrogen bonds with O···O distances of 2.780(2) − 3.063(2) Å and O-H···O angles of 150(1) − 179(1)° excluding a bifurcated bond. The interstitial water molecule displays a distorted tetrahedral environment of O atoms and accepts and donates each two hydrogen bonds. The crystal structure exhibits a C2/c pseudosymmetry for the [Be4(PO4)3(OH)3]4- layers and the Ca atoms. However, the disposition of the water molecules and an asymmetric hydrogen bond pattern involving OH groups as well as H2O molecules are decisive for the lowering of the symmetry of the structure to the true space group P21/n.

Stable perylene diimide radical/alkylamine complex linked by asymmetric [CO⋯H⋯N]−1 -type strong H-bond and its color switching properties

Radical anions of electron-deficient systems are widely used, but they are easily reoxidized upon exposure to air. Therefore, the stabilization of radical anions under ambient conditions is of great significance, but still remains a scientific challenge. Here, perylene diimide radical anion species is stabilized by an asymmetric anionic low barrier strong hydrogen bond, which is reported firstly. The exchange of a hydrogen atom between one hydrogen atom in nitrogen atom of alkyl amine and the oxygen atom of the carbonyl on perylene diimide radical anion occurs to form such asymmetric anionic type strong hydrogen bond. This bond energy of hydrogen bond is evaluated by the apparent activation energy of thermal decomposition, and it is about 50 kcal/mol. The geometric states in this hydrogen bond depend on external conditions, including solvents and pH value, which will cause the change of their photophysical properties. The hydrogen bond complex shows excellent pH-responsive color switching performance based on the difference in geometric states of this hydrogen bond.

Ab initio investigation of H-bond disordering in δ-AlOOH

\ensuremath{\delta}-AlOOH (\ensuremath{\delta}) is a high-pressure hydrous phase that participates in the deep geological water cycle. At 0 GPa, \ensuremath{\delta} has asymmetric hydrogen bonds (H bonds). Under pressure, it exhibits H-bond disordering, tunneling, and finally, H-bond symmetrization at \ensuremath{\sim}18 GPa. This study investigates these 300 K pressure-induced state changes in \ensuremath{\delta} with ab initio calculations. H-bond disordering in \ensuremath{\delta} was modeled using supercell multiconfiguration quasiharmonic calculations. We examine (a) energy barriers for proton jumps, (b) the pressure dependence of phonon frequencies, (c) 300 K compressibility, (d) neutron diffraction pattern anomalies, and (e) compare ab initio bond lengths with measured ones. Such thorough and systematic comparisons indicate that (a) proton ``disorder'' has a restricted meaning when applied to \ensuremath{\delta}. Nevertheless, H bonds are disordered between 0 and 8 GPa, and a gradual change in H-bond configuration results in enhanced compressibility. (b) Several structural and vibrational anomalies at \ensuremath{\sim}8 GPa are consistent with the disappearance of a particular (HOC-12) H-bond configuration and its change into another one (HOC-11*). (c) Between 8 and 11 GPa, H-bond configuration (HOC-11*) is generally ordered, at least in short- to midrange scale. (d) Between 11.5 and 18 GPa, H-bond lengths approach a critical value that impedes compression, resulting in decreased compressibility. In this pressure range, especially approaching H-bond symmetrization at \ensuremath{\sim}18 GPa, anharmonicity and tunneling should play an essential role in the proton dynamics. Further simulations accounting for these effects are desirable to clarify the protons' state in this pressure range.

Tracing the Anharmonicity and Superionic Phase Transition of Hydrous FeO2H

The weak x-ray scattering of hydrogen (H) has brought major challenges to the characterization of superionic transitions in high-pressure ice, hydrides, and hydroxides. Combining first-principles molecular dynamics and simulated nuclear magnetic resonance (NMR) spectroscopy, we investigated the behavior of the hydroxyl bonding and structural transitions in the hydrous FeO2H between 300 and 2750 K and up to 130 GPa. Evidence show that an intermediate plastic state with regional H diffusion and anharmonic O-H vibration exists in between the ordinary solid and the superionic phase. The intermediate state features asymmetric hydrogen bonds and anharmonic vibrations, which are readily distinguished from the high-temperature superionic phase. Our work shows NMR is a more sensitive probe to detect H diffusion in superionic solids even in the extreme conditions of Earth’s deep interiors.

Crystal structure of 2-{[5-amino-1-(phenyl-sulfon-yl)-1H-pyrazol-3-yl]-oxy}-1-(4-methyl-phen-yl)ethan-1-one.

In the title compound, C18H17N3O4S, the pyrazole ring is planar, with the sulfur atom lying 0.558 (1) Å out of the ring plane. The NH2 group is involved in an intra-molecular hydrogen bond to a sulfonyl oxygen atom; its other hydrogen atom forms an asymmetric three-centre hydrogen bond to the two oxygen atoms of the -O-CH2-C=O- grouping, via the 21 screw axis, forming a ribbon structure parallel to the b axis. Translationally adjacent, coplanar ribbons form a layer parallel to (10).

Symmetry Breaking in an Excited Quadrupolar Acridine-Dione Derivative Driven by Hydrogen Bonding.

An acridine-dione derivative (3,3,11,11-tetramethyl-8,16-diphenyl-3,4,8,10,11,12,13,16-octahydroacridino[4,3-c]acridine-1.9(2H,5H)dion) with quadrupolar motif has been synthesized and its stationary and transient spectra have been measured. Stationary absorption and fluorescence spectra as well as nonstationary spectra show no signs of symmetry breaking (SB) in aprotic solvents, even of high polarity. The specific features of SB are revealed in alcohol solvents through a considerable red shift of stationary fluorescence spectra and the appearance of a new excited state absorption band in transient absorption spectra. SB is due to the formation of asymmetric strong hydrogen bonds, mainly on one side of the molecule. An unexpected regularity of symmetry breaking is found in mixtures of aprotic dimethylformamide and protic methanol, where methanol acts as a fluorescence quencher. It is revealed that there is no quenching as long as the methanol concentration is less than the critical value of 9 M. This leads to the conclusion that SB in such mixtures is possible only if the concentration of the protic solvent exceeds a certain threshold value.

Neutron structures of Leishmania mexicana triosephosphate isomerase in complex with reaction-intermediate mimics shed light on the proton-shuttling steps.

Triosephosphate isomerase (TIM) is a key enzyme in glycolysis that catalyses the interconversion of glyceraldehyde 3-phosphate and dihydroxy-acetone phosphate. This simple reaction involves the shuttling of protons mediated by protolysable side chains. The catalytic power of TIM is thought to stem from its ability to facilitate the deprotonation of a carbon next to a carbonyl group to generate an enediolate intermediate. The enediolate intermediate is believed to be mimicked by the inhibitor 2-phosphoglycolate (PGA) and the subsequent enediol intermediate by phosphoglycolohydroxamate (PGH). Here, neutron structures of Leishmania mexicana TIM have been determined with both inhibitors, and joint neutron/X-ray refinement followed by quantum refinement has been performed. The structures show that in the PGA complex the postulated general base Glu167 is protonated, while in the PGH complex it remains deprotonated. The deuteron is clearly localized on Glu167 in the PGA-TIM structure, suggesting an asymmetric hydrogen bond instead of a low-barrier hydrogen bond. The full picture of the active-site protonation states allowed an investigation of the reaction mechanism using density-functional theory calculations.

Asymmetric Hydrogen-Bonding Structure at a Water/Ice Interface

The interface between liquid water and the basal plane of crystal ice Ih at the melting point temperature is investigated via molecular dynamics (MD) simulations to examine the molecular structure ...

Studying the hydrogen atom position in the strong-short intermolecular hydrogen bond of pure and 5-substituted 9-hydroxyphenalenones by invariom refinement and ONIOM cluster computations

Abstract The solid-state structures of three H-bonded enol forms of 5-substituted 9-hydroxyphenalenones were investigated to accurately determine the H atom positions of the intramolecular hydrogen bond. For this purpose, single-crystal X-ray diffraction (SC-XRD) data were evaluated by invariom-model refinement. In addition, QM/MM computations of central molecules in their crystal environment show that results of an earlier standard independent atom model refinement, which pointed to the presence of a resonance-assisted hydrogen bond in unsubstituted 9-hydroxyphenalone, are misleading: in all our three and the earlier solid-state structures the lowest energy form is that of an asymmetric hydrogen bond (CS form). Apparent differences of results from SC-XRD and other analytical methods are explained.

Investigation of hexakis[2-formylphenoxy]cyclotriphosphazene structure by single crystal X-ray diffraction and computer simulation

Crystallization of hexakis [2-formylphenoxy]cyclotriphosphazene was carried out from its melt and its solution. It was found that single crystals of this compound could be obtained via the slow crystallization from a chloroform–ethanol mixture. The melting point of such crystals was determined by the DSC method. These crystals have been for the first time investigated using the single crystal X-ray diffraction analysis. It was found that the phosphazene cycle in hexakis [2-formylphenoxy]cyclotriphosphazene is not planar in contrast to the starting hexachlorocyclotriphosphazene. The results acquired by X-ray diffraction were used in theoretical calculations of the characteristics of molecule. It was revealed that the spatial configuration of substituents in hexakis [2-formylphenoxy]cyclotriphosphazene is highly symmetrical towards the phosphazene cycle. There are π-stacking interactions between some aromatic cycles. The molecular framework is formed mainly by the C⋯H, C⋯C and H⋯H intramolecular interactions. A deformation of the phosphazene cycle arises due to asymmetric intramolecular hydrogen bonds between the nitrogen atoms of phosphazene cycle and the hydrogen atoms of aromatic rings. Performed structural calculations revealed the diameter of a sphere circumscribing the phosphazene molecule, which was 1.5 nm. These results of structural investigations may be of interest for the molecular design, theoretical prediction of the properties of new compounds, synthesis of coordination compounds, and nanotechnology.

Symmetry of Hydrogen Bonds in Two Enols in Solution.

The enols of 4-cyano-2,2,6,6-tetramethyl-3,5-heptanedione and of nitromalonamide were prepared as statistical mixtures of 18O n ( n = 0, 1, 2) isotopologues. The symmetries of their hydrogen bonds were probed by isotopic perturbation of their 13CO NMR signals. The former mixture shows a total of four signals, due to both intrinsic and perturbation isotope shifts. Therefore, that enol is a mixture of tautomers with an asymmetric hydrogen bond. In contrast, the mixture of isotopologues of nitromalonamide enol shows only two signals, due to an intrinsic isotope shift. Therefore, this is the first case, to be compared with the FHF- anion, of a neutral species with a single symmetric structure in solution and with a centered hydrogen.

New high-pressure phases in MOOH (M = Al, Ga, In)

A unique phase, belonging to an orthorhombic crystal system (Pbca, Z = 8), is proposed in AlOOH using crystal structure searches based on an evolutionary genetic algorithm method, combined with density functional theory. This phase features a nonlinear asymmetric doubly covalent hydrogen-bond and metal cations that are sixfold oxygen coordinated. Unlike the earlier proposed monoclinic phase, the stability region of Pbca (166–189 GPa) lies well below the pressure of decomposition to Al2O3+ice X (287 GPa). In GaOOH the Pbca-type phase is not energetically favorable at any pressure. In the course of evaluating the breakdown of GaOOH to its constituent oxides, we have found a new phase of Ga2O3 (U2S3-type). In InOOH, Pbca is energetically favorable over a narrow pressure interval (12–17 GPa). Also in InOOH, we find a new tetragonal structure (P4̄21m, Z = 4) stable above 51 GPa. This phase has nonlinear asymmetric hydrogen-bonds and metal cations that are sevenfold oxygen coordinated. Phonon calculations confirm the vibrational stability of the new phases and show that the high-pressure polymorphs of AlOOH are likely to be important carriers of water into the deep lower mantles of Earth and rocky super-Earths.

Unique Structures and Vibrational Spectra of Protic Ionic Liquids Confined in TiO2 Slits: The Role of Interfacial Hydrogen Bonds.

The ionic liquid (IL)/titanium dioxide (TiO2) interface exists in many application systems, such as nanomaterial synthesis, catalysis, and electrochemistry systems. The nanoscale interfacial properties in the above systems are a common issue. However, directly detecting the interfacial properties of nanoconfined ILs by experimental methods is still challenging. To help better learn about the interfacial issue, molecular dynamics simulations have been performed to explore the structures, vibration spectra, and hydrogen bond (HB) properties at the IL/TiO2 interface. Ethylammonium nitrate (EAN) ILs confined in TiO2 slit pores with different pore widths were studied. A unique vibrational spectrum appeared for EAN ILs confined in a 0.7 nm TiO2 slit, and this phenomenon is related to interfacial hydrogen bonds (HBs). An analysis of the HB types indicated that the interfacial NH3+ group of the cations was in an asymmetric HB environment in the 0.7 nm TiO2 slit, which led to the disappearance of the symmetric N-H stretching mode. In addition, the significant increase in the HB strength between NH3+ groups and the TiO2 surface slowed down the stretching vibration of the N-H bond, resulting in one peak in the vibrational spectra at a lower frequency. For the first time, our simulation work establishes a molecular-level relationship between the vibrational spectrum and the local HB environment of nanoconfined ILs at the IL/TiO2 interface, and this relationship is helpful for interface design in related systems.

Hydrogen-Bond Symmetrization of δ-AlOOH**Supported by the National Natural Science Foundation of China under Grant Nos U1232204, 41473056, 11422431 and 11634001, the National Key Research and Development Program of China under Grant No 2016YFA0300901, and the National Basic Research Program of China under Grant No 2013CB934600.

The δ-AlOOH can transport water into the deep mantle along cold subducting slab geotherm. We investigate the hydrogen-bond symmetrization behavior of δ-AlOOH under the relevant pressure-temperature condition of the lower mantle using ab initio molecular dynamics (MD). The static symmetrization pressure of 30.0 GPa can be reduced to 17.0 GPa at 300 K by finite-temperature (T) statistics, closer to the experimental observation of ∼10.0 GPa. The symmetrization pressure obtained by MD simulation is related to T by P (GPa) + 13.9 (GPa) = 0.01 (GPa/K) × T (K). We conclude that δ-AlOOH in the lower mantle exists with symmetric hydrogen bond from its birthplace, or someplace slightly deeper, to the core-mantle boundary (CMB) along cold subducting slab geotherm. The bulk modulus decreases with T and increases anomalously upon symmetrization: for δ-AlOOH with asymmetric hydrogen bond, and for δ-AlOOH with symmetric hydrogen bond. Our results provide an important insight into the existent form and properties of δ-AlOOH in the lower mantle.

Predicting the Position of the Hydrogen Atom in the Short Intramolecular Hydrogen Bond of the Hydrogen Maleate Anion from Geometric Correlations

The position of the hydrogen atom inside the strong and short intramolecular hydrogen bond of the hydrogen maleate anion strongly varies depending on the crystalline environment. Therefore, it has not been possible in the past to accurately determine it using X-ray diffraction data although there are 292 hydrogen maleate crystal structures with different cations in the literature. In this study, a geometric correlation for the accurate prediction of the hydrogen position in the short intramolecular hydrogen bond is presented. The results used to derive the correlation are obtained from low-temperature neutron-diffraction studies on nine different hydrogen maleate salts that span the whole range from perfectly symmetric to highly asymmetric intramolecular hydrogen bonds. Since the only variable in the correlation as derived from the neutron data is the O···O distance, the hydrogen atom position in question can subsequently be predicted using information that is accurately available from routine X-ray data....

Nanomechanical Properties of Polymorphic Human Islet Amyloid Polypeptide Protofibrils in the Multiple Physiological and Mechanical Conditions

Fibrillar and oligomeric amyloids are the origin of neuro-degenerative and degenerative diseases as type II diabetes, Alzheimer's diseases, and so forth. The common properties of amyloids are located near functional cells, not easily degraded, and disrupt their own functions. These amyloids had polymorphic characteristics under physiological conditions such as thermal effect, pH, ionic strength, metal ions and internal fluctuations. Developed from denatured and misfolded amyloid monomers, polymorphic amyloids are mainly existed as parallel or antiparallel composition along to fibril axis and lateral thickness composition by adding unit amyloid protofilament through the experimental techniques. Despite experimental effort of polymorphic structures of amyloid proteins, there are some lacks of knowledge that relationship between structural composition of polymorphic amyloids and their stabilities in detail. The mechanical characterization as bending, stretching can give insight for understanding the structure-property relationship of amyloid protofilaments. Considering that amyloids are developed through the repetitive fragmentation and elongation mechanisms, it is crucial to understand the structural stabilities of polymorphic amyloid protofibrils. Here, we reported the polymorphic characteristics of hIAPP amyloid protofibrils in mechanical insight via equilibrium and steered molecular dynamics (MD and SMD). Through the principal component analysis of polymorphic hIAPP protofibrils after equilibrium MD simulations, we found the different deformation mode (i.e. bending, stretching and torsion) of polymorphic hIAPP protofibrils. Using eigenvalue analysis, antiparallel models had considerable structural stability than parallel models due to the asymmetric hydrogen bond network composition. Furthermore, by applying the constant force bending and constant velocity tensile SMD simulations, we found the dominant material characteristics that homo composition had ductile feature, while hetero composition had brittle characteristics. We provide the relationship between structural composition and their properties, which are related to growth mechanism of amyloids. Our study also provides the possibilities for the basic template for functional biomaterials in the future.

First principles calculation of the elasticity of ice VIII and X

The elastic constants of ice VIII and ice X phases under pressure have been determined at static 0 K conditions using first principles calculation. A step-like increase of the elastic constants of ice VIII phase occurred at 100-110 GPa due to hydrogen bond symmetrization. The elastic constants, and the pressure dependencies of these constants, of ice X and VIII are completely distinct. Due to these differences, these two phases can be distinguished on the basis of the elastic behavior. Conversely, the experimental elastic constant of C11 of ice VII gradually changes from an ice VIII like asymmetric hydrogen bond to a symmetric bond character within a wide pressure range. This finding suggests that the transition from ice VII to ice X starts around 30 GPa and completes at 110 GPa.