Symmetric Hydrogen Bonds Research Articles

DNA-Like Duplex Structures Derived from Chemistry Based on 2’-Deoxy-Cytidine: A New Model for Base-Specific Inhibition of G and C on DNA and RNA Level

The new epigenetic elements 5-hydroxymethyl-dC, 5-formyl-dC, and 5-car- boxy-dC may be considered as intermediates of an active demethylation process. A comprehensive mechanistic model is given for the C-C bond cleavage focused on the chemistry within the DNA duplex structure. In addition we register spin-off chemistry of this process in evaluating new duplex systems closely related to natural DNA and RNA concerning their hydrogen-bond symmetrization. A model is composed for a base-specific inhibition of G and C on the DNA and RNA level. C-G combinations are of general importance in controlling the dynamics of gene expression. In some way the suggested model systems are related to antisense oligonucleotides (ASOs).

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.

Entanglement and co-tunneling of two equivalent protons in hydrogen bond pairs.

A theoretical study is reported of a system of two identical symmetric hydrogen bonds, weakly coupled such that the two mobile protons can move either separately (stepwise) or together (concerted). It is modeled by two equivalent quartic potentials interacting through dipolar and quadrupolar coupling terms. The tunneling Hamiltonian has two imaginary modes (reaction coordinates) and a potential with a single maximum that may turn into a saddle-point of second order and two sets of (inequivalent) minima. Diagonalization is achieved via a modified Jacobi-Davidson algorithm. From this Hamiltonian the mechanism of proton transfer is derived. To find out whether the two protons move stepwise or concerted, a new tool is introduced, based on the distribution of the probability flux in the dividing plane of the transfer mode. While stepwise transfer dominates for very weak coupling, it is found that concerted transfer (co-tunneling) always occurs, even when the coupling vanishes since the symmetry of the Hamiltonian imposes permanent entanglement on the motions of the two protons. We quantify this entanglement and show that, for a wide range of parameters of interest, the lowest pair of states of the Hamiltonian represents a perfect example of highly entangled quantum states in continuous variables. The method is applied to the molecule porphycene for which the observed tunneling splitting is calculated in satisfactory agreement with experiment, and the mechanism of double-proton tunneling is found to be predominantly concerted. We show that, under normal conditions, when they are in the ground state, the two porphycene protons are highly entangled, which may have interesting applications. The treatment also identifies the conditions under which such a system can be handled by conventional one-instanton techniques.

Hydrogen-Bond Symmetrization Breakdown and Dehydrogenation Mechanism of FeO2H at High Pressure.

The cycling of hydrogen plays an important role in the geochemical evolution of our planet. Under high-pressure conditions, asymmetric hydroxyl bonds tend to form a symmetric O-H-O configuration in which H is positioned at the center of two O atoms. The symmetrization of O-H bonds improves their thermal stability and as such, water-bearing minerals can be present deeper in the Earth's lower mantle. However, how exactly H is recycled from the deep mantle remains unclear. Here, we employ first-principles free-energy landscape sampling methods together with high pressure-high temperature experiments to reveal the dehydrogenation mechanism of a water-bearing mineral, FeO2H, at deep mantle conditions. Experimentally, we show that ∼50% H is released from symmetrically hydrogen-bonded ε-FeO2H upon transforming to a pyrite-type phase (Py-phase). By resolving the lowest-energy transition pathway from ε-FeO2H to the Py-phase, we demonstrate that half of the O-H bonds in the mineral rupture during the structural transition, leading toward the breakdown of symmetrized hydrogen bonds and eventual dehydrogenation. Our study sheds new light on the stability of symmetric hydrogen bonds during structural transitions and provides a dehydrogenation mechanism for hydrous minerals existing in the deep mantle.

The Origin of Hierarchical Structure Formation in Highly Grafted Symmetric Supramolecular Double-Comb Diblock Copolymers.

Involving supramolecular chemistry in self-assembling block copolymer systems enables design of complex macromolecular architectures that, in turn, could lead to complex phase behavior. It is an elegant route, as complicated and sensitive synthesis techniques can be avoided. Highly grafted double-comb diblock copolymers based on symmetric double hydrogen bond accepting poly(4-vinylpyridine)-block-poly(N-acryloylpiperidine) diblock copolymers and donating 3-nonadecylphenol amphiphiles are realized and studied systematically by changing the molecular weight of the copolymer. Double perpendicular lamellae-in-lamellae are formed in all complexes, independent of the copolymer molecular weight. Temperature-resolved measurements demonstrate that the supramolecular nature and ability to crystallize are responsible for the formation of such multiblock-like structures. Because of these driving forces and severe plasticization of the complexes in the liquid crystalline state, this supramolecular approach can be useful for steering self-assembly of both low- and high-molecular-weight block copolymer systems.

Hydrogen bond symmetrization and elastic constants under pressure of δ-AlOOH

The elastic constants of δ-AlOOH have been calculated for applied pressures in the range 0–40 GPa using three exchange-correlation functionals, i.e. PBEsol, TCAsol and PBE. PBEsol and TCAsol, which describe the geometry of this system very well, give similar results, while the PBE values are smaller, a consequence of the fact that the PBE lattice parameters are too large. In agreement with the experiments, the calculations show that at low pressure the axial compressibility is greater in the b direction and smaller in the c direction, while the opposite is true at high pressure. This change takes place 5 GPa before the calculated hydrogen bond symmetrization transition. Combining this result with those reported in the experimental papers, one obtains a strong indication that symmetrization takes place at about 15 GPa, in excellent agreement with the PBEsol and TCAsol predictions.

Thermal and nuclear quantum effects in the hydrogen bond dynamical symmetrization phase transition of δ-AlOOH

We conducted ab initio molecular dynamics simulations of the δ phase of the hydrous mineral aluminium oxide hydroxide (AlOOH) at ambient temperature and high pressure. Nuclear quantum effects were included through a Langevin dynamics in a bath of quantum harmonic oscillators. We confirm that under increasing pressure δ-AlOOH undergoes a phase transition from a P 2 1 nm structure with asymmetric and disordered O–H bonds to a stiffer Pnnm phase with symmetric hydrogen bonds, which should be stable within the pressure and temperature ranges typical for the Earth’s mantle. The transition is initially triggered by proton tunneling, which makes the mean proton position to coincide with the midpoint of the O–O distance, at pressures as low as 10 GPa. However, only at much larger pressures, around 30 GPa as previously found by other calculations, the Pnnm phase with symmetric hydrogen bonds is stable from the classical point of view. The transition is also characterized through the analysis of the H–O stretching modes, which soften considerably and fade out around 10 GPa in the P 2 1 nm structure, when thermal and nuclear quantum effects are taken into account in the simulations. At variance, the harmonic picture is not adequate to describe the highly anharmonic effective potential that is seen by the protons at the transition. Finally, we propose that the picture of a dynamical transition to the high-symmetry and proton-centered Pnnm phase, which is brought about by the onset of proton tunneling, could be confirmed by quasi-elastic neutron scattering and vibrational spectroscopy under pressure.

Structural, elastic, and vibrational properties of phase H: A first-principles simulation**Project supported by the Key Laboratory of Earthquake Prediction, Institute of Earthquake Science, China Earthquake Administration (CEA) (Grant Nos. 2016IES010104 and 2012ES0408) and the National Natural Science Foundation of China (Grant Nos. 41174071, 41273073, 41373060, and 41573121).

Phase H (MgSiOH, one of the dense hydrous magnesium silicates (DHMSs), is supposed to be vital to transporting water into the lower mantle. Here the crystal structure, elasticity and Raman vibrational properties of the two possible structures of phase H with Pm and symmetry under high pressures are evaluated by first-principles simulations. The cell parameters, elastic and Raman vibrational properties of the Pm symmetry become the same as the symmetry at GPa. The symmetrization of hydrogen bonds of the Pm symmetry at GPa results in this structural transformation from Pm to . Seismic wave velocities of phase H are calculated in a range from 0 GPa to 100 GPa and the results testify the existence and stability of phase H in the lower mantle. The azimuthal anisotropies for phase H are , ( symmetry) and , ( symmetry) at 0 GPa, and increase to , ( symmetry) and , (Pm symmetry) at 30 GPa. The maximum direction for phase H is [101] and the minimum direction is [110]. The anisotropic results of seismic wave velocities imply that phase H might be a source of seismic anisotropy in the lower mantle. Furthermore, Raman vibrational modes are analyzed to figure out the effect of symmetrization of hydrogen bonds on Raman vibrational pattern and the dependence of Raman spectrum on pressure. Our results may lead to an in-depth understanding of the stability of phase H in the mantle.

Stable high-pressure phases in the H-S system determined by chemically reacting hydrogen and sulfur

Synchrotron X-ray diffraction and Raman spectroscopy have been used to study chemical reactions of molecular hydrogen (H2) with sulfur (S) at high pressures. We find theoretically predicted Cccm and Im-3m H3S to be the reaction products at 50 and 140 GPa, respectively. Im-3m H3S is a stable crystalline phase above 140 GPa and it transforms to R3m H3S on pressure release below 140 GPa. The latter phase is (meta)stable down to at least 70 GPa where it transforms to Cccm H3S upon annealing (T<1300 K) to overcome the kinetic hindrance. Cccm H3S has an extended structure with symmetric hydrogen bonds at 50 GPa and upon decompression it experiences a transformation to a molecular mixed H2S-H2 structure below 40 GPa without any apparent change in the crystal symmetry.

Hydrogen bonds in the vicinity of the special pair of the bacterial reaction center probed by hydrostatic high-pressure absorption spectroscopy

Using the native bacteriochlorophyll a pigment cofactors as local probes, we investigated the response to external hydrostatic high pressure of reaction center membrane protein complexes from the photosynthetic bacterium Rhodobacter sphaeroides. Wild-type and engineered complexes were used with a varied number (0, 1 or 2) of hydrogen bonds that bind the reaction center primary donor bacteriochlorophyll cofactors to the surrounding protein scaffold. A pressure-induced breakage of hydrogen bonds was established for both detergent-purified and membrane-embedded reaction centers, but at rather different pressures: between 0.2 and 0.3GPa and at about 0.55GPa, respectively. The free energy change associated with the rupture of the single hydrogen bond present in wild-type reaction centers was estimated to be equal to 13–14kJ/mol. In the mutant with two symmetrical hydrogen bonds (FM197H) a single cooperative rupture of the two bonds was observed corresponding to an about twice stronger bond, rather than a sequential rupture of two individual bonds.

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.

Stabilizing Superacid Anions: The New [H(S4O13)2]3− Anion in the Crystal Structure of Li3[H(S4O13)2

The unique hydrogenium-bis-tetrasulfate anion [H(S4 O13 )2 ]3- in the crystal structure of Li3 [H(S4 O13 )2 ] (monoclinic, P21 /n (No. 14), Z=2, a=552.46(4) pm, b=939.70(6) pm, c=1876.6(1) pm, β=97.492(3)°, V=965.9(1)⋅106 pm3 ) is the longest protonated polysulfate chain ever observed. Very strong symmetrical hydrogen bonds are a bold feature of the crystal structure. The protonation of a very weak base such as [S4 O13 ]2- and accordingly the stabilization of the first base of the superacid H2 S4 O13 is a significant success towards the still elusive polysulfuric acids.

New Raman measurements for H2O ice VII in the range of 300 cm-1 to 4000 cm-1 at pressures up to 120 GPa.

Raman spectroscopic measurements for H2O ice VII have been conducted to 120 GPa at 300 K in the spectroscopic range of 300-4000 cm-1. Both moissanite and diamond anvils were used for the experiments. This overcomes the problems of overlapping spectra between the diamond anvil and sample, which had prevented the observation of the stretching modes at pressures higher than ∼23 GPa in all previous measurements. The new results reveal many bands which have not been reported before. The pressure dependences of the Raman modes show anomalous changes at 13-15, ∼27, ∼44, ∼60, and 90 GPa, implying possible structural changes at these pressures. The new results demonstrate that the predicted symmetric hydrogen bond phase X transition does not occur below 120 GPa.

Proton-shared hydrogen bond: Promoting generation of novel triradicals, and serving as phosphorescent and magnetic switch

Stable organic radicals have many essential and unique applications in chemistry, biology and materials. In order to probe new radical materials, we report herein a novel type of solid-state stable diarylmethyl monoradicals, which were synthesized via facile “one-pot” approach. The monoradicals can be easily converted to solid-state stable diarylmethyl triradicals promoted by unusual and symmetric proton-shared hydrogen bond. Diarylmethyl triradicals reveal higher ambient phosphorescent quantum yield and enhanced near-infrared absorption. Moreover, switchable phosphorescent and magnetic transformation between triradicals and monoradicals controlled by proton-shared hydrogen bond avails to develop switch materials. Unprecedentedly, the proton-shared hydrogen bond serves as a phosphorescent and magnetic switch. The present work provides a new access to synthesize stable diaryl-methyl (-alkyl) radicals and develop new switchable materials.

Stability of the different AlOOH phases under pressure

The pressure effects on three different AlOOH structures (α, γ, and δ phases) are systematically analyzed by density functional theory with different exchange and correlation energy functional approximations, namely two local, two generalized-gradient approximation (GGA), and two GGA for solids (GGAsol). Phase stability, compressibility and hydrogen bond evolution are studied in a range of pressures from 0 to 30 GPa. In general, the use of GGAsol functionals is mandatory in order to have the correct phase stability order, a good description of the hydrogen bonds, and a close agreement with the experimental lattice parameters at the various pressures. Pressure-induced hydrogen-bond symmetrization is found in γ and δ phases at high compression, while the hydrogen bonds in the α phase remain asymmetric. A detailed analysis of the uncertainties on the values of the bulk moduli and their pressure derivative at zero pressure deduced by fitting calculated or experimental (P,V) data is also presented.

Quantum hydrogen-bond symmetrization in the superconducting hydrogen sulfide system.

The quantum nature of the proton can crucially affect the structural and physical properties of hydrogen compounds. For example, in the high-pressure phases of H2O, quantum proton fluctuations lead to symmetrization of the hydrogen bond and reduce the boundary between asymmetric and symmetric structures in the phase diagram by 30 gigapascals (ref. 3). Here we show that an analogous quantum symmetrization occurs in the recently discovered sulfur hydride superconductor with a superconducting transition temperature Tc of 203 kelvin at 155 gigapascals--the highest Tc reported for any superconductor so far. Superconductivity occurs via the formation of a compound with chemical formula H3S (sulfur trihydride) with sulfur atoms arranged on a body-centred cubic lattice. If the hydrogen atoms are treated as classical particles, then for pressures greater than about 175 gigapascals they are predicted to sit exactly halfway between two sulfur atoms in a structure with Im3m symmetry. At lower pressures, the hydrogen atoms move to an off-centre position, forming a short H-S covalent bond and a longer H···S hydrogen bond in a structure with R3m symmetry. X-ray diffraction experiments confirm the H3S stoichiometry and the sulfur lattice sites, but were unable to discriminate between the two phases. Ab initio density-functional-theory calculations show that quantum nuclear motion lowers the symmetrization pressure by 72 gigapascals for H3S and by 60 gigapascals for D3S. Consequently, we predict that the Im3m phase dominates the pressure range within which the high Tc was measured. The observed pressure dependence of Tc is accurately reproduced in our calculations for the phase, but not for the R3m phase. Therefore, the quantum nature of the proton fundamentally changes the superconducting phase diagram of H3S.

Charge-Assisted Hydrogen-Bonded Networks of NH4+ and [Co(NH3)6]3+ with the New Linker Anion of 4-Phosphono-Biphenyl-4′-Carboxylic Acid

The new linker molecule 4-phosphono-biphenyl-4′-carboxylic acid (H2O3P-(C6H4)2-COOH, H3BPPA) has been structurally elucidated in hydrogen-bonded networks with the ammonium cation NH4(H2BPPA)(H3BPPA) (1) and the hexaamminecobalt(III) cation [Co(NH3)6](BPPA)·4H2O (2). The protic O-H and N-H hydrogen atoms were found and refined in the low-temperature single-crystal X-ray structures. The hydrogen bonds in both structures are so-called charge-assisted; that is, the H-bond donor and/or acceptor carry positive and/or negative ionic charges, respectively. The H-bonded network in 1 consists of one formally mono-deprotonated 4-phosphonato-biphenyl-4′-carboxylic acid group; that is, a H2BPPA− anion and a neutral H3BPPA molecule, which together form a 3D hydrogen-bonded network. However, an almost symmetric resonance-assisted hydrogen bond (RAHB) bond [O···H = 1.17 (3) and 1.26 (3) Å, O···H···O = 180 (3)°] signals charge delocalization between the formal H2BPPA− anion and the formally neutral H3BPPA molecule. Hence, the anion in 1 is better formulated as [H2BPPA···H···H2BPPA]−. In the H-bonded network of 2 the 4-phosphonato-biphenyl-4′-carboxylic acid is triply deprotonated, BPPA3−. The [Co(NH3)6]3+ cation is embedded between H-bond acceptor groups, –COO− and –PO3− and H2O molecules. The incorporation of sixteen H2O molecules per unit cell makes 2 an analogue of the well-studied guanidinium sulfonate frameworks.

Hydrogen Bond Symmetrization in Glycinium Oxalate under Pressure.

The study of hydrogen bonds near symmetrization limit at high pressures is of importance to understand proton dynamics in complex bio-geological processes. We report here the evidence of hydrogen bond symmetrization in the simplest amino acid-carboxylic acid complex, glycinium oxalate, at moderate pressures of 8 GPa using in-situ infrared and Raman spectroscopic investigations combined with first-principles simulations. The dynamic proton sharing between semioxalate units results in covalent-like infinite oxalate chains. At pressures above 12 GPa, the glycine units systematically reorient with pressure to form hydrogen-bonded supramolecular assemblies held together by these chains.

Iodine salts of the pharmaceutical compound agomelatine: the effect of the symmetric H-bond on amide protonation

The search for new solid forms of an active pharmaceutical ingredient (API) is an important step in drug development. Often, an API has low water solubility, which then leads to low oral bioavailability. The problem can be solved by salt formation. One such API is agomelatine (AG), a melatonergic antidepressant. The aim of this work is to prepare iodide(s) of this compound. Three structurally different iodides of agomelatine were synthesized: agomelatine hydriodide trihydrate (AGI), agomelatine hemitriiodide (AG2I3) and agomelatine hemitriiodide iodine (AGI2). Their structures were solved from single-crystal X-ray diffraction data. In all of the structures, the agomelatine molecule was positively charged. Specifically, the amide oxygen was protonated, and in two of the structures (AG2I3 and AGI2), a symmetric hydrogen bond was formed. However, agomelatine is an amidic compound, and since amides are generally considered as neutral, in addition to SXRD, we present data from solid state NMR and the ΔpKa calculation to support the proton transfer and the salt formation.

Novel Superconducting Phases of HCl and HBr under High Pressure: An Ab Initio Study

The novel superconducting C2/m phases of HCl and HBr were predicted using the developed particle swarm optimization algorithm for crystal structure prediction. The calculated results showed that the phase transition from P-1 to C2/m phases occurred at 250 and 120 GPa for HCl and HBr, respectively. Hydrogen bond symmetrization was observed in the newly predicted C2/m phase. No imaginary phonon frequencies in the whole Brillouin zone indicated that the C2/m phases of HCl and HBr were dynamically stable. In addition, the C2/m phase of HBr was the most stable structure, which rejected the earlier hypotheses of elemental decomposition into bromine and hydrogen. Perturbative linear response calculations predicted that the critical temperature Tc of the C2/m phase of HCl could reach 20 K at 250 GPa.