Hydrogen-bond geometry and its isotope effect in crystals with OHO bonds—revisited

Layered CrO2·nH2O as a cathode material for aqueous zinc-ion batteries: ab initio study

Aqueous zinc-ion batteries are considered potential large-scale energy storage systems due to their low cost, environmentally friendly nature, and high safety. However, the development of high energy density cathode materials and uncertain reaction mechanisms remains a major challenge. In this work, the reaction mechanism, discharge voltage and diffusion properties of layered CrO2 as a cathode material for aqueous zinc-ion batteries were studied using first-principles calculations, and the effect of pre-intercalated structural water on the electrochemical performance of CrO2 electrodes is also discussed. The results show that CrO2 exhibits high average discharge voltages (2.65 V for H insertion (pH = 7) and 1.97 V for Zn insertion) and medium theoretical capacities (319 mA h g-1 (H and Zn)). The H intercalation voltage strongly depends on the pH value of the electrolyte. The H/Zn co-insertion mechanism occurs at low hydrogen concentrations (c(H) ≤ 0.125), where the initial insertion of H reduces the total amount of subsequent Zn insertion. For the substrate containing structured water (CrO2·nH2O, n ≥ 0.5), the average voltage of Zn insertion is significantly increased, while the average voltage of H slightly decreases. In addition, the pre-intercalated water strategy significantly improved the diffusion properties of H and Zn. This study shows that layered CrO2·nH2O is a promising cathode material for aqueous zinc-ion batteries, and also provides theoretical guidance for the development of high-performance cathode materials for aqueous zinc-ion batteries.

Phosphine oxides as NMR and IR spectroscopic probes for geometry and energy of PO···H–A hydrogen bonds

In this work we evaluate the possibility to use the NMR and IR spectral properties of P=O group to estimate the geometry and strength of hydrogen bonds which it forms...

Reliability of the Phonon Density of States Determined by Real-Coded Genetic Algorithm from Heat Capacities of Benzoic Acid Crystals

Constant-pressure heat capacities (C_Ps) of crystalline benzoic acid (BAh) and its deuterated analogue (C₆H₅COOD, BAd) were measured by adiabatic calorimetry, and the phonon density (g(ω)) of states was determined from their C_P data using a real-coded genetic algorithm (RCGA) with just generation gap + real-coded ensemble cross-over. The distribution of g(ω) was in reasonable agreement with the spectroscopic one observed for molecular vibration modes, indicating sufficient reliability of g(ω) determined by the RCGA. Based on the fact that C_Ps reveals an inverse-isotope effect in the temperature range 30-130 K, the determined g(ω)s were used to investigate the molecular mechanism of the effect: g(ω) of BAd revealed blue shifts in the ranges of ω = 80-100 and 150-230 K, as referred to that of BAh. It was suggested from the combined considerations on g(ω) and spectroscopic results that an anticooperative correlation exists between O-H···O hydrogen bonds and interdimer interactions in BA.

Theoretical study of the H/D isotope effect of CH4/CD4 adsorption on a Rh(111) surface using a combined plane wave and localized basis sets method

Using our CPLB method, we elucidate that the adsorption distance and adsorption energy of CH₄ on the Rh(111) surface are shorter and larger than those of CD₄, which is in reasonable agreement with the corresponding H/D isotope trend in experiments.

High-pressure sapphire capillary cell for synchrotron single-crystal X-ray diffraction measurements to 1500 bar

A new sapphire capillary pressure cell for single-crystal X-ray diffraction measurements at moderate pressures (200−1500 bar; 1 bar = 100 kPa) has been developed and optimized for use on beamline I19 at Diamond Light Source. The three-component cell permits optical centring of the crystal and in situ pressure modification to a precision of 1 bar. Compression of hexamethylenetetramine and its deuterated analogue to 1000 bar was performed, showcasing the accuracy and precision of the measurements, and highlighting evidence of a geometric isotope effect.

Hydrated Metal Ion Salts of the Weakly Coordinating Fluoroanions PF6-, TiF62-, B12F122-, Ga(C2F5)4-, B(3,5-C6H3(CF3)2)4-, and Al(OC(CF3)3)4-. In Search of the Weakest HOH···F Hydrogen Bonds

FTIR spectra of microcrystalline samples of 11 metal ion salt hydrates of a variety of weakly coordinating fluoroanions are reported. The compounds studied were Li(H₂O)₄(Al(OC(CF₃)₃)₄), Li(H₂O)(B(3,5-C₆H₃(CF₃)₂)₄), Li(H₂O)_n(Ga(C₂F₅)₄), Li(H₂O)(PF₆), Li₂(H₂O)₂(TiF₆), Li₂(H₂O)₄(B₁₂F₁₂), Na(H₂O)(PF₆), Na₂(H₂O)₂(B₁₂F₁₂), K₂(H₂O)₂(B₁₂F₁₂), Rb₂(H₂O)₂(B₁₂F₁₂), Cs₂(H₂O)(B₁₂F₁₂), and their partially or completely deuterated isotopologs and isotopomers. The O-D···F hydrogen bonds in Li(HOD)(H₂O)₃(Al(OC(CF₃)₃)₄) (ν(OD) = 2706 cm^-1), Li(HOD)(B(3,5-C₆H₃(CF₃)₂)₄) (ν(OD) = 2705 cm^-1), and Li(HOD)(H₂O)_n(Ga(C₂F₅)₄) (ν(OD) = 2697 cm^-1) rival HOD absorbed in polyvinylidene difluoride (ν(OD) = 2696 cm^-1) and HOD···FCH₃ in a frozen Ar matrix (ν(OD) = 2685 cm^-1) for the weakest hydrogen bonds between a water molecule and an F atom in any compound. As weak as they are, minor differences in O-H···F hydrogen bonds in the same fluoroanion salt can be distinguished spectroscopically. Uncoupled HOD molecules in asymmetric F···HOD···F' hydrogen bonding environments in Rb⁺, Cs⁺, Mg²⁺, and Co²⁺ hydrates of B₁₂F₁₂^2- gave rise to two observable ν(OD) bands even though the two R(O···F) distances differ by only 0.010(4) Å (Mg²⁺), 0.033(2) Å (Co²⁺), 0.074(4) Å (Rb⁺), and 0.106(6) Å (Cs⁺). A plot of ν(OD) for hydrates with a single uncoupled HOD molecule per metal ion (e.g., Li(HOD)(H₂O)₃(Al(OC(CF₃)₃)₄)) vs R(O···F) distance from single-crystal X-ray or neutron diffraction structures was prepared. The ν(OD) values range from 2305 to 2706 cm^-1 and the R(O···F) distances range from 2.58 to 3.17 Å. The plot consists of 53 {ν(OD), R(O···F)} data points, 23 of which are new and have ν(OD) > 2600 cm^-1, in contrast to a 1994 ν(OD) vs R(O···F) plot with 28 data points, none of which had ν(OD) > 2600 cm^-1. There is a clear and significant difference between the new ν(OD) vs R(O···F) plot and a literature ν(OD) vs R(O···O) plot for hydrates containing O-D···O hydrogen bonds. For a given ν(OD) stretching frequency, the exponential regression curves show that R(O···F) is typically 0.1-0.2 Å shorter than R(O···O), in harmony with the lower basicity and smaller size of F atoms vs O atoms.

Geometric H/D isotope effect in a series of organic salts involving short O–H⋯O hydrogen bonds between carboxyl and carboxylate groups

Noticeable elongations of donor–acceptor distances upon deuteration are confirmed in short O–H⋯O hydrogen bonds between carboxyl and carboxylate groups.

Perceptible isotopic effect in 3D-framework of α-glycine at low temperatures

Glycine, the most fundamental amino acid, albeit studied for many decades, has kept researchers captivated with interesting structural variations relevant to important biological, astrophysical and technological applications. We report here a noticeable effect of deuteration on the three dimensional hydrogen bonding network of α-glycine using low temperature infrared absorption studies in a wide spectral range, corroborated with Raman scattering studies. These systematic studies in the range 300-4.2 K have demonstrated a relatively compact assembly of glycine molecules in the three dimensional bilayered structure of hydrogenated glycine (gly-h) at low temperatures. This is inferred from a remarkable temperature effect in the weak intra-bilayer hydrogen bond ~ along the b-axis, which strengthens upon cooling. A pronounced increase in the intensity of NH₃ torsional and NH stretching modes has been observed. This is accompanied with a large rate of stiffening and softening respectively of these modes upon cooling and a change in slope across 210 K and 80 K. In contrast, the D---O hydrogen bond lengths in fully deuterated isotope (gly-d), as estimated using empirical correlation, show that the weak intra-bilayer hydrogen bond is not strengthened upon cooling down to 180 K, whereas the stronger intra-layer hydrogen bonds in the ac-plane become further strong. The ND₃ torsional vibrations show no temperature effect. This implies a relatively stable two dimensional layered structure formed by strongly hydrogen bonded glycine sheets in the ac-plane. Below 180 K, similar qualitative trends have been obtained for the hydrogen bond lengths in the two isotopes. In addition, temperature induced variation of the characteristic "indicator" band of zwitterionic gly-h and gly-d has also been reported.

Direct observation of symmetrization of hydrogen bond in δ-AlOOH under mantle conditions using neutron diffraction

At ambient pressure, the hydrogen bond in materials such as ice, hydrates, and hydrous minerals that compose the Earth and icy planets generally takes an asymmetric O-H···O configuration. Pressure significantly affects this configuration, and it is predicted to become symmetric, such that the hydrogen is centered between the two oxygen atoms at high pressure. Changes of physical properties of minerals relevant to this symmetrization have been found; however, the atomic configuration around this symmetrization has remained elusive so far. Here we observed the pressure response of the hydrogen bonds in the aluminous hydrous minerals δ-AlOOH and δ-AlOOD by means of a neutron diffraction experiment. We find that the transition from P2₁nm to Pnnm at 9.0 GPa, accompanied by a change in the axial ratios of δ-AlOOH, corresponds to the disorder of hydrogen bond between two equivalent sites across the center of the O···O line. Symmetrization of the hydrogen bond is observed at 18.1 GPa, which is considerably higher than the disorder pressure. Moreover, there is a significant isotope effect on hydrogen bond geometry and transition pressure. This study indicates that disorder of the hydrogen bond as a precursor of symmetrization may also play an important role in determining the physical properties of minerals such as bulk modulus and seismic wave velocities in the Earth's mantle.

Geometric isotope effect of deuteration in a hydrogen-bonded host-guest crystal

Deuteration of a hydrogen bond by replacing protium (H) with deuterium (D) can cause geometric changes in the hydrogen bond, known as the geometric H/D isotope effect (GIE). Understanding the GIEs on global structures and bulk properties is of great importance to study structure–property relationships of hydrogen-bonded systems. Here, we report a hydrogen-bonded host–guest crystal, imidazolium hydrogen terephthalate, that exemplifies striking GIEs on its hydrogen bonds, phases, and bulk dielectric transition property. Upon deuteration, the donor–acceptor distance in the O–H···O hydrogen bonds in the host structure is found to increase, which results in a change in the global hydrogen-bonded supramolecular structure and the emergence of a new phase (i.e., isotopic polymorphism). Consequently, the dynamics of the confined guest, which depend on the internal pressure exerted by the host framework, are substantially altered, showing a downward shift of the dielectric switching temperature.

Deuterating a hydrogen bond can change the bond’s geometry, a phenomenon known as the geometric isotope effect (GIE). Here, the authors find that a hydrogen-bonded host–guest crystal, imidazolium hydrogen terephthalate, exhibits significant GIE on its hydrogen bonds, changing its crystal phases and bulk dielectric properties.

Temperature-induced polymorphism in methyl stearate

Different temperature conditions can induce different crystallisation behaviours of methyl stearate. Three new polymorphs have been identified and structural characterised.

Theoretical study of the H/D isotope effect on phase transition of hydrogen-bonded organic conductor κ-H3(Cat-EDT-TTF)2

κ-H₃(Cat-EDT-TTF)₂ (H-TTF) is a hydrogen-bonded π-electron system. Only its isotopologue, D-TTF, shows the phase transition. We obtained a symmetric single-well effective-PEC for H-TTF and low-barrier effective-PEC for D-TTF.

Determination of Hydrogen Bond Structure in Water versus Aprotic Environments To Test the Relationship Between Length and Stability

Hydrogen bonds profoundly influence the architecture and activity of biological macromolecules. Deep appreciation of hydrogen bond contributions to biomolecular function thus requires a detailed understanding of hydrogen bond structure and energetics and the relationship between these properties. Hydrogen bond formation energies (ΔGf) are enormously more favorable in aprotic solvents than in water, and two classes of contributing factors have been proposed to explain this energetic difference, focusing respectively on the isolated and hydrogen-bonded species: (I) water stabilizes the dissociated donor and acceptor groups much better than aprotic solvents, thereby reducing the driving force for hydrogen bond formation; and (II) water lengthens hydrogen bonds compared to aprotic environments, thereby decreasing the potential energy within the hydrogen bond. Each model has been proposed to provide a dominant contribution to ΔGf, but incisive tests that distinguish the importance of these contributions are lacking. Here we directly test the structural basis of model II. Neutron crystallography, NMR spectroscopy, and quantum mechanical calculations demonstrate that O-H···O hydrogen bonds in crystals, chloroform, acetone, and water have nearly identical lengths and very similar potential energy surfaces despite ΔGf differences >8 kcal/mol across these solvents. These results rule out a substantial contribution from solvent-dependent differences in hydrogen bond structure and potential energy after association (model II) and thus support the conclusion that differences in hydrogen bond ΔGf are predominantly determined by solvent interactions with the dissociated groups (model I). These findings advance our understanding of universal hydrogen-bonding interactions and have important implications for biology and engineering.

Solid-state MAS NMR studies of Brønsted acid sites in zeolite H-Mordenite

(17)O-(1)H double resonance NMR spectroscopy was used to study the local structure of zeolite H-Mordenite. Different contact times were used in cross-polarization magic angle spinning (CPMAS) NMR, CP rotational-echo double resonance (CP-REDOR) NMR, and heteronuclear correlation (HETCOR) NMR spectroscopy to distinguish between Brønsted acid sites with different O-H distances. The accessibility of the various Brønsted acid sites was quantified by adsorbing the basic probe molecule trimethylphosphine in known amounts. On the basis of these experiments, locations of different Brønsted acid sites in H-Mordenite (H-MOR) were proposed. The use of (17)O chemical shift correlations to help assign sites is discussed.

Interpretation of intermolecular geometric isotope effect in hydrogen bonds: nuclear orbital plus molecular orbital study

The intermolecular geometric isotope effect (GIE) in hydrogen bond A-X···B (X = H and D) is investigated theoretically using the nuclear orbital plus molecular orbital (NOMO) theory. To interpret the GIE in terms of physically meaningful energy components such as electrostatic and exchange-repulsion interactions, the reduced variational space self-consistent-field method is extended to the NOMO scheme. The intermolecular GIE is analyzed as a two-stage process: the intramolecular bond shrinkage and the intermolecular bond elongation. According to the isotopic shifts of energy components described by the NOMO/MP2 method, the intermolecular GIE is approximately interpreted as a process reducing the exchange-repulsion interaction after the decrease of electrostatic interaction.

Hydrogen bond coupling in the ketosteroid isomerase active site

Hydrogen bond networks are key elements of biological structure and function. Nevertheless, their structural properties are challenging to assess within complex macromolecules. Hydrogen-bonded protons are not observed in the vast majority of protein X-ray structures, and static crystallographic models provide limited information regarding the dynamical coupling within hydrogen bond networks. We have brought together 1.1-1.3 A resolution X-ray crystallography, (1)H NMR, site-directed mutagenesis, and deuterium isotope effects on the geometry and chemical shifts of hydrogen-bonded protons to probe the conformational coupling of hydrogen bonds donated by Y16 and D103 in the oxyanion hole of bacterial ketosteroid isomerase. Our results suggest a robust physical coupling of the equilibrium structures of these two hydrogen bonds such that a lengthening of one hydrogen bond by as little as 0.01 A results in a shortening of the neighbor by a similar magnitude. Furthermore, the structural rearrangements detected by NMR in response to mutations within the active site hydrogen bond network can be explained on the basis of the observed coupling. The results herein elucidate fundamental structural properties of hydrogen bonds within the idiosyncratic environment of an enzyme active site and provide a foundation for future experimental and computational explorations of the role of coupled motions within hydrogen bond networks.

Hydrogen bond dynamics in the active site of photoactive yellow protein

Hydrogen bonds play major roles in biological structure and function. Nonetheless, hydrogen-bonded protons are not typically observed by X-ray crystallography, and most structural studies provide limited insight into the conformational plasticity of individual hydrogen bonds or the dynamical coupling present within hydrogen bond networks. We report the NMR detection of the hydrogen-bonded protons donated by Tyr-42 and Glu-46 to the chromophore oxygen in the active site of the bacterial photoreceptor, photoactive yellow protein (PYP). We have used the NMR resonances for these hydrogen bonds to probe their conformational properties and ability to rearrange in response to nearby electronic perturbation. The detection of geometric isotope effects transmitted between the Tyr-42 and Glu-46 hydrogen bonds provides strong evidence for robust coupling of their equilibrium conformations. Incorporation of a modified chromophore containing an electron-withdrawing cyano group to delocalize negative charge from the chromophore oxygen, analogous to the electronic rearrangement detected upon photon absorption, results in a lengthening of the Tyr-42 and Glu-46 hydrogen bonds and an attenuated hydrogen bond coupling. The results herein elucidate fundamental properties of hydrogen bonds within the complex environment of a protein interior. Furthermore, the robust conformational coupling and plasticity of hydrogen bonds observed in the PYP active site may facilitate the larger-scale dynamical coupling and signal transduction inherent to the biological function that PYP has evolved to carry out and may provide a model for other coupled dynamic systems.

Structure-property relationships in the crystals of the smallest amino acid: an incoherent inelastic neutron scattering study of the glycine polymorphs

Incoherent inelastic neutron scattering spectra for the three crystalline polymorphs (alpha- P2(1)/n, beta- P2(1), gamma- P3(1)) of glycine (C2H5NO2) at temperatures between 5 and 300 K (using the time-of-flight (ToF) spectrometer NEAT at HMI) and at pressures from ambient up to 1 GPa (using the ToF spectrometer IN6 at the ILL) were measured. Significant differences in the band positions and their relative intensities in the density of states (DoS) were observed for the three polymorphs, which can be related to the different intermolecular interactions. The mean-squared displacement, <u(2)>(T), dependence reveals a change in dynamic properties at about the same temperature (150 K) for all the three forms, which can be related to the reorientation of the NH3 group. Besides, a dynamic transition in beta-glycine at about 230-250 K on cooling was also observed, supporting previously obtained adiabatic calorimetry data. This behavior is similar to that already observed in amorphous solids, on approaching the glass transition temperatures, as well as in biological systems. It suggests the onset of degrees of freedom most likely related to transitions between slightly different conformational orientations. The DoS obtained as a function of pressure has confirmed the stability of the alpha-form with respect to pressure and also depicted a sign of the previously reported reversible beta-beta' glycine phase transition in between 0.6 and 0.8 GPa. Moreover, a remarkable kinetic effect in the pressure-induced phase transition in gamma-glycine was revealed. After the sample was kept at 0.8 GPa for an hour in the neutron beam, an irreversible transition into a high-pressure form (different from the beta'-form) occurred, although previously in X-Ray diffraction and Raman spectroscopy experiments a gamma- to delta-glycine phase transition was observed above 3.5 GPa only.

Car-Parrinello and path integral molecular dynamics study of the hydrogen bond in the chloroacetic acid dimer system

We have studied the double proton transfer (DPT) reaction in the cyclic dimer of chloroacetic acid using both classical and path integral Car-Parrinello molecular dynamics. We also attempt to quantify the errors in the potential energy surface that arise from the use of a pure density functional. In the classical dynamics a clear reaction mechanism can be identified, where asynchronized DPT arises due to coupling between the O-H stretching oscillator and several low energy intermolecular vibrational modes. This mechanism is considerably altered when quantum tunneling is permitted in the simulation. The introduction of path integrals leads to considerable changes in the thermally averaged molecular geometry, leading to shorter and more centered hydrogen bond linkages.

17O Magic Angle Spinning NMR Studies of Brønsted Acid Sites in Zeolites HY and HZSM-5

High-resolution 17O/1H double resonance NMR spectra were obtained for two zeolites, one with a low Si/Al ratio (zeolite HY) and one with a high Si/Al ratio (HZSM-5), to investigate their local structure and Brønsted acidity. Two different oxygen signals, corresponding to Brønsted acid sites in supercages and sodalite cages of zeolite HY were readily resolved in the two-dimensional (2-D) 1H-17O heteronuclear correlation (HETCOR) NMR spectra allowing the 17O isotropic chemical shift (deltaCS) and quadrupolar coupling parameters (quadrupolar coupling constant, QCC, and asymmetry parameter, eta) for the two oxygen atoms to be extracted. Similar experiments for HZSM-5 showed that the sites in this system are associated with a much larger distribution in NMR parameters than found in HY. 17O-1H rotational echo double resonance (REDOR) NMR was applied to probe the O-H distances in zeolites HY and HZSM-5. Weaker 17O-1H dephasing was observed for zeolite HZSM-5 in comparison to that of HY, consistent with longer O-H bonds and/or increased proton mobility.

X-ray diffraction and inelastic neutron scattering study of 1:1 tetramethylpyrazine chloranilic acid complex: temperature, isotope, and pressure effects

The x-ray diffraction studies of the title complex were carried out at room temperature and 14 K for H/D (in hydrogen bridge) isotopomers. At 82 K a phase transition takes place leading to a doubling of unit cells and alternation of the hydrogen bond lengths linking tetramethylpyrazine (TMP) and chloranilic acid molecules. A marked H/D isotope effect on these lengths was found at room temperature. The elongation is much smaller at 14 K. The infrared isotopic ratio for O-H(D)...N bands equals to 1.33. The four tunnel splittings of methyl librational ground states of the protonated complex required by the structure are determined at a temperature T=4.2 K up to pressures P=4.7 kbars by high resolution neutron spectroscopy. The tunnel mode at 20.6 microeV at ambient pressure shifts smoothly to 12.2 microeV at P=3.4 kbars. This is attributed to an increase of the strength of the rotational potential proportional to r(-5.6). The three other tunnel peaks show no or weak shifts only. The increasing interaction with diminishing intermolecular distances is assumed to be compensated by a charge transfer between the constituents of deltae/e approximately 0.02 kbar(-1). The phase transition observed between 3.4 and 4.7 kbars leads to increased symmetry with only two more intense tunneling bands. In the isotopomer with deuterated hydrogen bonds and P=1 bar all tunnel intensities become equal in consistency with the low temperature crystal structure. The effect of charge transfer is confirmed by a weakening of rotational potentials for those methyl groups whose tunnel splittings were independent of pressure. Density functional theory calculations for the model TMP.(HF)2 complex and fully ionized molecule TMP+ point out that the intramolecular rotational potential of methyl groups is weaker in the charged species. They do not allow for the unequivocal conclusions about the role of the intermolecular charge transfer effect on the torsional frequencies.

Origins of isotopomeric polymorphism

The complex formed between 4-methylpyridine and pentachlorophenol (4MPPCP) crystallises in a triclinic space group. If the same complex is synthesized from deuterated pentachlorophenol, it crystallizes in an entirely different monoclinic polymorph. Using solid-state NMR of samples synthesized with a full range of deuteration levels, crystallized from solution or the melt, and in the presence or absence of seeds, we have confirmed that the isotopomers indeed have different thermodynamically stable crystal structures. The roots of this phenomenon of isotopomeric polymorphism apparently lie in the differences in hydrogen bonding between the polymorphs. The triclinic form has a relatively short hydrogen bond. High-field solid-state NMR shows both the 1H chemical shift and the 2H electric quadrupole coupling of the hydrogen involved in the bond to be strongly temperature-dependent, indicating a low-lying excited state of the hydrogen bond longitudinal vibration. Inelastic neutron scattering of isotopomers of 4MPPCP has allowed us to identify the three orthogonal vibrational modes of the hydrogen in the hydrogen bond, at 29.7, 145, and 205 meV (240, 1168, and 1651 cm(-1)). The longitudinal mode is the lowest in energy, and it indicates a slightly asymmetric low-barrier double-well potential. Intrinsic to such potentials is a very small difference in zero-point energies (ZPEs) between the protonated and deuterated forms. As a contrast, the monoclinic form has a comparatively normal hydrogen bond, in which the proton and deuteron ZPEs should be different by approximately 500 cm(-1). A scenario can be envisaged where the triclinic protonated form is lower in energy than the monoclinic protonated form, but the triclinic deuterated form is higher in energy than the monoclinic deuterated form. This evidently accounts for the difference in relative stabilities of the two forms upon isotope substitution.