Hydrogen-bonding Topologies Research Articles

Statistical Equivalence of Quantum Chemical Methods for Energy Distribution in Water Clusters.

Methods of quantum chemistry are instrumental in understanding molecular structures and properties. However, the results demonstrate significant variability, which is difficult to predict and rationalize. The fundamental question is whether some molecular systems exhibit properties invariant with respect to the computational method. The idea explored here is that collective properties of statistical ensembles should be more robust than characteristics of individual molecules and their arbitrary sets. This effect is demonstrated for the complete set of hydrogen-bond topologies of the dodecahedral water cluster (H2 O)20 . Non-Gaussian energy distributions produced by various methods have the same functional form despite strong differences in mean values and standard deviations. The conclusion is tested on methods of different complexity and origin employing a number of criteria. A linear mapping between the energies produced by different methods is discussed. The significance of the results is in establishing a collective equivalence property of quantum chemical methods.

HBcompare: Classifying Ligand Binding Preferences with Hydrogen Bond Topology.

This paper presents HBcompare, a method that classifies protein structures according to ligand binding preference categories by analyzing hydrogen bond topology. HBcompare excludes other characteristics of protein structure so that, in the event of accurate classification, it can implicate the involvement of hydrogen bonds in selective binding. This approach contrasts from methods that represent many aspects of protein structure because holistic representations cannot associate classification with just one characteristic. To our knowledge, HBcompare is the first technique with this capability. On five datasets of proteins that catalyze similar reactions with different preferred ligands, HBcompare correctly categorized proteins with similar ligand binding preferences 89.5% of the time. Using only hydrogen bond topology, classification accuracy with HBcompare surpassed standard structure-based comparison algorithms that use atomic coordinates. As a tool for implicating the role of hydrogen bonds in protein function categories, HBcompare represents a first step towards the automatic explanation of biochemical mechanisms.

Anomalies and Local Structure of Liquid Water from Boiling to the Supercooled Regime as Predicted by the Many-Body MB-pol Model.

For the past 50 years, researchers have sought molecular models that can accurately reproduce water's microscopic structure and thermophysical properties across broad ranges of its complex phase diagram. Herein, molecular dynamics simulations with the many-body MB-pol model are performed to monitor the thermodynamic response functions and local structure of liquid water from the boiling point down to deeply supercooled temperatures at ambient pressure. The isothermal compressibility and isobaric heat capacity show maxima near 223 K, in excellent agreement with recent experiments, and the liquid density exhibits a minimum at ∼208 K. A local tetrahedral arrangement, where each water molecule accepts and donates two hydrogen bonds, is found to be the most probable hydrogen-bonding topology at all temperatures. This work suggests that MB-pol may provide predictive capability for studies of liquid water's physical properties across broad ranges of thermodynamic states, including the so-called water's "no man's land" which is difficult to probe experimentally.

The extensive solid-form landscape of sulfathiazole: hydrogen-bond topology and node shape

Patterns of hydrogen bonds are described in a set of 101 crystal structures containing sulfathiazole. Topological analysis of the hydrogen-bond nets is augmented by comparison of the shapes of the nodes extracted from each net.

Structural Characterization of Protonated Water Clusters Confined in HZSM-5 Zeolites.

A molecular description of the structure and behavior of water confined in aluminosilicate zeolite pores is a crucial component for understanding zeolite acid chemistry under hydrous conditions. In this study, we use a combination of ultrafast two-dimensional infrared (2D IR) spectroscopy and ab initio molecular dynamics (AIMD) to study H2O confined in the pores of highly hydrated zeolite HZSM-5 (∼13 and ∼6 equivalents of H2O per Al atom). The 2D IR spectrum reveals correlations between the vibrations of both terminal and H-bonded O-H groups and the continuum absorption of the excess proton. These data are used to characterize the hydrogen-bonding network within the cluster by quantifying single-, double-, and non-hydrogen-bond donor water molecules. These results are found to be in good agreement with the statistics calculated from an AIMD simulation of an H+(H2O)8 cluster in HZSM-5. Furthermore, IR spectral assignments to local O-H environments are validated with DFT calculations on clusters drawn from AIMD simulations. The simulations reveal that the excess charge is detached from the zeolite and resides near the more highly coordinated water molecules in the cluster. When they are taken together, these results unambiguously assign the complex IR spectrum of highly hydrated HZSM-5, providing quantitative information on the molecular environments and hydrogen-bonding topology of protonated water clusters under extreme confinement.

The order/disorder phase transition of hypophosphorous acid H3PO2

Abstract Hypophosphorous acid, H3PO2 is dimorphic with a phase transition in the 200–225 K range. The H3PO2 molecules are connected by hydrogen bonding to infinite chains extending in the [100] direction. In the high-temperature phase (P21212, Z ′ = 1 2 ${Z}^{\prime }=\frac{1}{2}$ ), the hydrogen bonds are disordered about a two-fold rotation axis. On cooling below the phase transition temperature, the hydrogen bonds become ordered, resulting in a symmetry reduction of the klassengleiche type of index 2. In the low-temperature phase (P212121, Z ′ = 1 ${Z}^{\prime }=1$ ), the c parameter is doubled with respect to the high-temperature phase. The hydrogen-bonding topology of the high- and low-temperature phases are double-infinite directed and undirected linear graphs, respectively.

Hydrogen Bonds, Topologies, Energy Frameworks and Solubilities of Five Sorafenib Salts.

Sorafenib (Sor) is an oral multi-kinase inhibitor, but its water solubility is very low. To improve its solubility, sorafenib hydrochloride hydrate, sorafenib hydrobromide and sorafenib hydrobromide hydrate were prepared in the mixed solvent of the corresponding acid solution, and tetrahydrofuran (THF). The crystal structures of sorafenib hydrochloride trihydrate (Sor·HCl.3H2O), 4-(4-{3-[4-chloro-3-(trifluoro-methyl)phenyl]ureido}phenoxy)-2-(N-methylcarbamoyl) pyridinium hydrochloride trihydrate, C21H17ClF3N4O3+·Cl−.3H2O (I), sorafenib hydrochloride monohydrate (Sor·HCl.H2O), C21H17ClF3N4O3+·Cl−.H2O (II), its solvated form (sorafenib hydrochloride monohydrate monotetrahydrofuran (Sor·HCl.H2O.THF), C21H17ClF3N4O3+·Cl−.H2O.C4H8O (III)), sorafenib hydrobromide (Sor·HBr), 4-(4-{3-[4-chloro-3-(trifluoro-methyl)phenyl]ureido}phenoxy)-2-(N-methylcarbamoyl) pyridinium hydrobromide, C21H17ClF3N4O3+·Br− (IV) and sorafenib hydrobromide monohydrate (Sor·HBr.H2O), C21H17ClF3N4O3+·Br−.H2O (V) were analysed. Their hydrogen bond systems and topologies were investigated. The results showed the distinct roles of water molecules in stabilizing their crystal structures. Moreover, (II) and (V) were isomorphous crystal structures with the same space group P21/n, and similar unit cell dimensions. The predicted morphologies of these forms based on the BFDH model matched well with experimental morphologies. The energy frameworks showed that (I), and (IV) might have better tabletability than (II) and (V). Moreover, the solubility and dissolution rate data exhibited an improvement in the solubility of these salts compared with the free drug.

Demystifying the Diffuse Vibrational Spectrum of Aqueous Protons Through Cold Cluster Spectroscopy.

The ease with which the pH is routinely determined for aqueous solutions masks the fact that the cationic product of Arrhenius acid dissolution, the hydrated proton, or H+(aq), is a remarkably complex species. Here, we review how results obtained over the past 30 years in the study of H+⋅(H2O)n cluster ions isolated in the gas phase shed light on the chemical nature of H+(aq). This effort has also revealed molecular-level aspects of the Grotthuss relay mechanism for positive-charge translocation in water. Recently developed methods involving cryogenic cooling in radiofrequency ion traps and the application of two-color, infrared-infrared (IR-IR) double-resonance spectroscopy have established a clear picture of how local hydrogen-bond topology drives the diverse spectral signatures of the excess proton. This information now enables a new generation of cluster studies designed to unravel the microscopic mechanics underlying the ultrafast relaxation dynamics displayed by H+(aq).

Disordered sodium alkoxides from powder data: crystal structures of sodium ethoxide, propoxide, butoxide and pentoxide, and some of their solvates

The crystal structures of sodium ethoxide (sodium ethanolate, NaOEt), sodium n-propoxide (sodium n-propanolate, NaO n Pr), sodium n-butoxide (sodium n-butanolate, NaO n Bu) and sodium n-pentoxide (sodium n-amylate, NaO n Am) were determined from powder X-ray diffraction data. NaOEt crystallizes in space group P 421 m, with Z = 2, and the other alkoxides crystallize in P4/nmm, with Z = 2. To resolve space-group ambiguities, a Bärnighausen tree was set up, and Rietveld refinements were performed with different models. In all structures, the Na and O atoms form a quadratic net, with the alkyl groups pointing outwards on both sides (anti-PbO type). The alkyl groups are disordered. The disorder becomes even more pronounced with increasing chain length. Recrystallization from the corresponding alcohols yielded four sodium alkoxide solvates: sodium ethoxide ethanol disolvate (NaOEt·2EtOH), sodium n-propoxide n-propanol disolvate (NaO n Pr·2 n PrOH), sodium isopropoxide isopropanol pentasolvate (NaO i Pr·5 i PrOH) and sodium tert-amylate tert-amyl alcohol monosolvate (NaO t Am· t AmOH, t Am = 2-methyl-2-butyl). Their crystal structures were determined by single-crystal X-ray diffraction. All these solvates form chain structures consisting of Na+, –O− and –OH groups, encased by alkyl groups. The hydrogen-bond networks diverge widely among the solvate structures. The hydrogen-bond topology of the i PrOH network in NaO i Pr·5 i PrOH shows branched hydrogen bonds and differs considerably from the networks in pure crystalline i PrOH.

Infrared spectroscopic study of hydrogen bonding topologies in the smallest ice cube

The water octamer with its cubic structure consisting of six four-membered rings presents an excellent cluster system for unraveling the cooperative interactions driven by subtle changes in the hydrogen-bonding topology. Despite prediction of many distinct structures, it has not been possible to extract the structural information encoded in their vibrational spectra because this requires size-selectivity of the neutral clusters with sufficient resolution to identify the contributions of the different isomeric forms. Here we report the size-specific infrared spectra of the isolated cold, neutral water octamer using a scheme based on threshold photoionization using a tunable vacuum ultraviolet free electron laser. A plethora of sharp vibrational bands features are observed. Theoretical analysis of these patterns reveals the coexistence of five cubic isomers, including two with chirality. The relative energies of these structures are found to reflect topology-dependent, delocalized multi-center hydrogen-bonding interactions. These results demonstrate that even with a common structural motif, the degree of cooperativity among the hydrogen-bonding network creates a hierarchy of distinct species. The implications of these results on possible metastable forms of ice are speculated.

Molecular interpretation of the non-Newtonian viscoelastic behavior of liquid water at high frequencies

Using classical as well as ab-initio molecular dynamics simulations, we calculate the frequency-dependent shear viscosity of pure water and water-glycerol mixtures. In agreement with recent experiments, we find deviations from Newtonian-fluid behavior in the THz regime. Based on an extension of the Maxwell model, we introduce a viscoelastic model to describe the observed viscosity spectrum of pure water. We find four relaxation modes in the spectrum which we attribute to i) hydrogen-bond network topology changes, ii) hydrogen-bond stretch vibrations of water pairs, iii) collective vibrations of water molecule triplets, and iv) librational excitations of individual water molecules. Our model quantitatively describes the viscoelastic response of liquid water on short timescales, where the hydrodynamic description via a Newtonian-fluid model breaks down.

Hydration in aqueous osmolyte solutions: the case of TMAO and urea.

The hydration and hydrogen-bond topology of small water solvated molecules such as the naturally occurring organic osmolytes trimethylamine N-oxide (TMAO) and urea are under intense investigation. We aim at furthering the understanding of this complex hydration by combining experimental oxygen K-edge excitation spectra with results from spectra calculated via the Bethe-Salpeter equation based on structures obtained from ab initio molecular dynamics simulations. Comparison of experimental and calculated spectra allows us to extract detailed information about the immediate surrounding of the solute molecules in the solvated state. We quantify and localize the influence of the solute on the hydrogen bond network of the water solvent and find spectroscopic fingerprints of a clear directional asymmetry around TMAO with strong and local kosmotropic influence around TMAO's NO head group and slight chaotropic influence around the hydrophobic methyl groups. The influence of urea on the local water network is qualitatively similar to that of TMAO but weaker in magnitude. The strongest influence of both molecules on the shape of the oxygen K-edge spectra is found in the first hydration shells.

A zinc(II) coordination polymer based on carboxyphenyl-terpyridine ligand with novel hydrogen-bond topology

A zinc(II) coordination polymer 1 has been solvothermally synthesized by mixing 4-(4-carboxyphenyl)-2, 2′: 6′, 2″-terpyridine (HL) and zinc salt, and characterized by powder and single crystal X-ray diffraction, thermogravimetric (TG) analyses, infrared spectra and elemental analyses. Complex 1 adopts 1D chain structure constructed by crosslinking Zn and L ligands. Interestingly, strong H-bond interactions between guest water and carboxyl group of L ligands result in the formation of novel 3, 3-connected network with point symbol (123). In addition, strong π⋯π interactions are also observed between different aromatic rings of L ligands which may help to enhance the framework stability. Moreover, the luminescent properties of 1 have also been investigated at room temperature.

Deconstructing water's diffuse OH stretching vibrational spectrum with cold clusters.

The diffuse vibrational envelope displayed by water precludes direct observation of how different hydrogen-bond topologies dictate the spectral response of individual hydroxy group (OH) oscillators. Using cold, isotopically labeled cluster ions, we report the spectral signatures of a single, intact water (H2O) molecule embedded at various sites in the clathrate-like cage structure adopted by the Cs+·(D2O)20 ion. These patterns reveal the site-dependent correlation between the frequencies of the two OH groups on the same water molecule and establish that the bound OH companion of the free OH group exclusively accounts for bands in the lower-energy region of the spectrum. The observed multiplet structures reveal the homogeneous linewidths of the fundamentals and quantify the anharmonic contributions arising from coupling to both the intramolecular bending and intermolecular soft modes.

Temperature Dependence of the Air/Water Interface Revealed by Polarization Sensitive Sum-Frequency Generation Spectroscopy.

The temperature dependence of the vibrational sum-frequency generation (vSFG) spectra of the air/water interface is investigated using many-body molecular dynamics (MB-MD) simulations performed with the MB-pol potential energy function. The vSFG spectra calculated for different polarization combinations are then analyzed in terms of molecular autocorrelation and cross-correlation contributions. To provide molecular-level insights into interfacial hydrogen-bonding topologies, which give rise to specific spectroscopic features, the vSFG spectra are further investigated by separating contributions associated with water molecules donating zero, one, or two hydrogen bonds to neighboring water molecules. This analysis suggests that the low frequency shoulder of the free OH peak which appears at ∼3600 cm-1 is primarily due to intermolecular couplings between both singly and doubly hydrogen-bonded molecules.

Cation Hydration in Supercritical NaOH and HCl Aqueous Solutions.

We present a study of the local atomic environment of the oxygen atoms in the aqueous solutions of NaOH and HCl under simultaneous high-temperature and high-pressure conditions. Experimental nonresonant X-ray Raman scattering core-level spectra at the oxygen K-edge show systematic changes as a function of temperature and pressure. These systematic changes are distinct for the two different solutes and are described well by calculations within the Bethe-Salpeter formalism for snapshots from ab initio molecular dynamics simulations. The agreement between experimental and simulation results allows us to use the computations for a detailed fingerprinting analysis in an effort to elucidate the local atomic structure and hydrogen-bonding topology in these relevant solutions. We observe that both electrolytes, especially NaOH, enhance hydrogen bonding and tetrahedrality in the water structure at supercritical conditions, in particular in the vicinity of the hydration shells. This effect is accompanied with the association of the HCl and NaOH molecules at elevated temperatures.

Ortho-Substituent Effects on Diphenylurea Packing Motifs

Hydrogen bonding between urea groups is a widely used motif in crystal engineering and supramolecular chemistry studies. In an effort to discern how the steric and electronic properties of substituents affect the molecular conformation and crystal packing of ortho-substituted N,N′-diphenylureas (oPUs), herein we report the synthesis, characterization, and polymorph screening of eight members of this family. Of the 16 total oPU structures known (including nine structures from this study and seven previously reported), only two are isostructural. These 16 structures are sorted into three general architecture types based on their hydrogen bond topologies. In Type I, urea molecules related by translation form linear one-dimensional (1D) hydrogen bonded chains. In Type II, urea molecules rotate about a 1D hydrogen bond axis forming twisted chains. Urea groups do not hydrogen bond to one another in Type III. Energy calculations performed at the B3LYP/6-31G(d,p) level show a higher rotational barrier about the amide bond in oPUs compared to meta-substituted diphenylureas (mPUs), which may explain the smaller range of torsion angles observed in oPUs compared to mPUs. Although ortho-substitution does not seem to limit the hydrogen bonding between urea groups in most cases, a notably higher percentage of oPU phases are polar compared to PUs with other substitution patterns. This suggests restricted conformations might offer some advantage in achieving acentric materials.

Polymorphism of the hydroxide perovskite Ga(OH)3 and possible proton-driven transformational behaviour

The crystal structure of hydroxide perovskite Ga(OH)3, the mineral sohngeite, has been determined for a natural sample by single-crystal XRD in space group P42/nmc to R 1 = 0.031, wR 2 = 0.071, GoF = 1.208, and for comparison also in space group P42/n to R 1 = 0.031, wR 2 = 0.073, GoF = 1.076. Unit cell parameters are a = 7.4546(2) A, c = 7.3915(2) A, V = 410.75(2) A3. The two structures are very similar and both have tilt system a + a + c −. The approximate positions of all H atoms in each structure have been refined. In the P42/nmc structure all five H sites are half-occupied, whereas in the P42/n structure four sites are half-occupied and one is fully occupied. The presence of five non-equivalent OH groups in sohngeite is confirmed by single-crystal Raman spectroscopy, but does not allow a choice between these two space groups to be made. There is only a single very weak violator of the c-glide of P42/nmc and the two refined structures are essentially the same, but are significantly different from that of the original description in which orthorhombic space group Pmn21 was reported with corresponding tilt system a 0 a 0 c +. It is argued here that such a structure is very implausible for a hydroxide perovskite. On heating sohngeite to 423 K, transformation to a cubic structure with $$Im\bar{3}$$ symmetry (a + a + a +) of the aristotype occurs. This cubic phase was recovered on cooling to 293 K without back-transformation to the tetragonal polymorph. As there is no continuous group/subgroup pathway from P42/nmc (or P42/n) to $$Im\bar{3}$$ , the transformation must be first-order, which is consistent with the large hysteresis observed. The change from the tetragonal to cubic structures involves a change in tilt system a + a + c − → a + a + a +, with a significant reconfiguration of hydrogen-bonding topology. The very different tilt systems and hydrogen-bonding configurations of the two polymorphs are responsible for hysteresis and metastable preservation of the cubic phase at 293 K. As the Ga(OH)6 octahedra of the low- and high-T polymorphs are very similar it is inferred that the transformation is driven by proton behaviour, presumably involving proton re-ordering.

Pressure-induced localisation of the hydrogen-bond network in KOH-VI.

Using a combination of ab initio crystal structure prediction and neutron diffraction techniques, we have solved the full structure of KOH-VI at 7 GPa. Rather than being orthorhombic and proton-ordered as had previously be proposed, we find that this high-pressure phase of potassium hydroxide is tetragonal (space group I4/mmm) and proton disordered. It has an unusual hydrogen bond topology, where the hydroxyl groups form isolated hydrogen-bonded square planar (OH)4 units. This structure is stable above 6.5 GPa and, despite being macroscopically proton-disordered, local ice rules enforce microscopic order of the hydrogen bonds. We suggest the use of this novel type of structure to study concerted proton tunneling in the solid state, while the topology of the hydrogen bond network could conceivably be exploited in data storage applications based solely on the manipulations of hydrogen bonds. The unusual localisation of the hydrogen bond network under applied pressure is found to be favored by a more compact packing of the constituents in a distorted cesium chloride structure.

Does Higher-Dimensional Hydrogen Bonding Guarantee a Smaller Thermal Expansion? A Thermal Expansion Study of an Interdigitated 1D and Interpenetrated 3D Hydrogen-Bonded Colored Dimorphic System

The 1:1:1 complex of benzene-1,3,5-tricarboxylic acid (BTA), 4,4′-methylenebis(2,6-dimethylaniline) (MBDA), and methanol has two polymorphic forms that can be regarded as synthon polymorphs. The hydrogen bond dimensionalities in the crystal structure of the two forms are different, and the forms have their own unique colors. The polymorph, with a three-dimensional hydrogen bond topology (3D form), forms an interpenetrated network and is violet in color, whereas the other polymorph, which is bright yellow in color, forms an interdigitated one-dimensional hydrogen bond topology (1D form). The volumetric expansion of the 3D form is comparable to that of the 1D form, but the anisotropy of expansion is found to be significantly higher in the 3D form than in its 1D counterpart. A structure–property correlation study of the dimorphic complex is presented in the context of their thermal expansion behavior and color.