Short Hydrogen Bond Research Articles

Mononuclear Alkali Metal Organoperoxides Stabilized by an NNNN‐Macrocycle and Short Hydrogen Bonds from ROOH Molecules

A series of light alkali metal organoperoxides [MOOR] (M=Li, Na, K; R=tBu, CMe2 Ph) were isolated in mononuclear form, aided by the tetradentate and neutral NNNN-type macrocycle Me4 TACD (L; Me4 [12]aneN4 =1,4,7,10-tetramethyl-1,4,7,10-tetraazacyclododecane) and strong hydrogen bonds from additional ROOH molecules. The Na and K compounds are characterized by short O-H⋅⋅⋅O contacts, in the case of the Na derivative as short as 2.41 Å.

Proton Network Flexibility Enables Robustness and Large Electric Fields in the Ketosteroid Isomerase Active Site.

Hydrogen-bond networks play vital roles in biological functions ranging from protein folding to enzyme catalysis. Here we combine electronic structure calculations and ab initio path integral molecular dynamics simulations, which incorporate both nuclear and electronic quantum effects, to show why the network of short hydrogen bonds in the active site of ketosteroid isomerase is remarkably robust to mutations along the network and how this gives rise to large local electric fields. We demonstrate that these properties arise from the network's ability to respond to a perturbation by shifting proton positions and redistributing electronic charge density. This flexibility leads to small changes in properties such as the partial ionization of residues and pKa isotope effects upon mutation of the residues, consistent with recent experiments. This proton flexibility is further enhanced when an extended hydrogen-bond network forms in the presence of an intermediate analogue, which allows us to explain the chemical origins of the large electric fields in the enzyme's active site observed in recent experiments.

Effect of cationic substitution on the double-well hydrogen-bond potential in [K1−x (NH4) x ]3H(SO4)2 proton conductors: a single-crystal neutron diffraction study

The structure of the mixed crystal [K1-x(NH4)x]3H(SO4)2 as obtained from single-crystal neutron diffraction is compared with the previously reported room-temperature neutron structure of crystalline K3H(SO4)2. The two structures are very similar, as indicated by the high value of their isostructurality index (94.8%). It was found that the replacement of even a small amount (3%) of K+ with NH4+ has a significant influence on the short strong hydrogen bond connecting the two SO42- ions. Earlier optical measurements had revealed that the kinetics of the superionic transition in the solid solution [K1-x(NH4)x]3H(SO4)2 are much faster than in K3H(SO4)2; this reported difference in the kinetics of the superionic phase transition in this class of crystal is explained on the basis of the difference in strength of the hydrogen-bond interactions in the two structures.

Probing the Menasemiquinone Binding Mode to Nitrate Reductase A by Selective 2 H and 15 N Labeling, HYSCORE Spectroscopy, and DFT Modeling.

In vivo specific isotope labeling at the residue or substituent level is used to probe menasemiquinone (MSK) binding to the quinol oxidation site of respiratory nitrate reductase A (NarGHI) from E. coli. 15 N selective labeling of His15 Nδ or Lys15 Nζ in combination with hyperfine sublevel correlation (HYSCORE) spectroscopy unambiguously identified His15 Nδ as the direct hydrogen-bond donor to the radical. In contrast, an essentially anisotropic coupling to Lys15 Nζ consistent with a through-space magnetic interaction was resolved. This suggests that MSK does not form a hydrogen bond with the side chain of the nearby Lys86 residue. In addition, selective 2 H labeling of the menaquinone methyl ring substituent allows unambiguous characterization of the 2 H-and hence of the 1 H-methyl isotropic hyperfine coupling by 2 H HYSCORE. DFT calculations show that a simple molecular model consisting of an imidazole Nδ atom in a hydrogen-bond interaction with a MSK radical anion satisfactorily accounts for the available spectroscopic data. These results support our previously proposed one-sided binding model for MSK to NarGHI through a single short hydrogen bond to the Nδ of His66, one of the distal heme axial ligands. This work establishes the basis for future investigations aimed at determining the functional relevance of this peculiar binding mode.

Compressibility and reversible amorphization of thaumasite Ca3Si(OH)6(CO3)(SO4)·12H2O pressurized in methanol–ethanol–H2O up to 5 GPa

The elastic and structure behavior of natural thaumasite compressed in methanol–ethanol–H2O up to 5 GPa was studied by synchrotron powder diffraction with a diamond anvil cell. In the pressure range between 0.0001 and 4.5 GPa, the compression is regular and slightly anisotropic, with a more rigid ab-plane coinciding with the orientation of hydrogen bonds and S–O, C–O bonds in anion groups. The corresponding bulk moduli derived from the third-order Birch–Murnaghan EoS fit are K a = 43(2), K c = 35(2), K T = 39(2) GPa. Rietveld refinements reveal some general features of the structure evolution of thaumasite, which are consistent with the observed elastic anisotropy. The compression within the ab-plane proceeds mainly at the expense of shortening of hydrogen bonds and much lesser decrease of C–O and S–O bonds. In the range of 0.0001–3 GPa the Ca–O polyhedra contract more rapidly along the c-axis as compared to the ab-plane. At about 5 GPa, thaumasite undergoes a reversible transformation to an amorphous phase. The observed behavior differs drastically with that studied previously using helium as the pressure medium, which suggests the effect of He penetration increasing the structure stiffness. Without helium support, the thaumasite structure is preserved only up to 4.5 GPa.

Anomalous dielectric response of short hydrogen bonds under pressure: the case of (Mn,Fe)2+AlPO4(OH)2H2O

An anomalous increase in the real part of dielectric response is observed in Mn0.5Fe0.5AlPO4(OH)2H2O while cooling to ~70 K. This is addressed to field-induced proton dynamics in a short hydrogen bond of 2.480(3) Å. The absence of discontinuities in heat capacity curves above the Néel temperature (TN ≈ 7 K) excludes a paraelectric to antiferroelectric phase transition. Upon the application of mild hydrostatic pressures below 1.6 GPa, the maximum in the dielectric response is shifted from 70 K to lower temperatures near 2 K. This explains a narrow correlation between proton transfer and the compression of the short hydrogen bond length.

Proton Transfer Rates in Ionized Hydrogen Chloride–Water Clusters: A Direct Ab Initio Molecular Dynamics Study

Reactions of the microhydrated hydrogen chloride radical cation, [HCl-(H2O)n]+ (n = 1-5), following the ionization of the parent neutral cluster were investigated by the direct ab initio molecular dynamics (AIMD) method to elucidate the cluster size dependence of the proton transfer (PT) rate in the ionized state. The ionization occurred from the HCl moiety of the clusters. The proton of HCl+ was transferred to the neighboring water molecule in the cluster. The time of PT was strongly dependent on the cluster size (n); the time of PT decreased with increasing n and reached a limiting value at n = 4-5 (the time of PT was ca. 7 fs). The acceleration of the PT rate was mainly caused by the shortness of the hydrogen bond between HCl+ and H2O in larger clusters, that is, a short hydrogen bond causes fast PT. The electrostatic effects of the water cluster further accelerated the rate of PT. After the first PT from HCl+ to H2O, the second PT (H3O+ + H2O →H2O + H3O+) was detected for n = 3-5. The times of the first and second PTs were calculated as 7-15 and 30-40 fs, respectively. The reaction mechanism was discussed based on the theoretical results.

A whole zoo of hydrogen bonds in one crystal structure: tris(isonicotinium) hydrogensulfate sulfate monohydrate.

Depending on the reaction partner, the organic ditopic molecule isonicotinic acid (Hina) can act either as a Brønsted acid or base. With sulfuric acid, the pyridine ring is protonated to become a pyridinium cation. Crystallization from ethanol affords the title compound tris(4-carboxypyridinium) hydrogensulfate sulfate monohydrate, 3C6H6NO2+·HSO4-·SO42-·H2O or [(H2ina)3(HSO4)(SO4)(H2O)]. This solid contains 11 classical hydrogen bonds of very different flavour and nonclassical C-H...O contacts. All N-H and O-H donors find at least one acceptor within a suitable distance range, with one of the three pyridinium H atoms engaged in bifurcated N-H...O hydrogen bonds. The shortest hydrogen-bonding O...O distance is subtended by hydrogensulfate and sulfate anions, viz. 2.4752 (19) Å, and represents one of the shortest hydrogen bonds ever reported between these residues.

An ordering phase transition, short hydrogen bonds and high Z' in the structure of Ni(Hpydc)2·3H2O.

The structure of Ni(Hpydc)2·3H2O (H2pydc = pyridine-2,6-dicarboxylic acid, also known as dipicolinic acid) has been reinvestigated at variable temperatures. At room temperature, it matches the known structure in the space group P21/c, but at 180 K it undergoes a phase transformation to a twinned structure in Cc. By 120 K, the structure is ordered and twinned with Z' = 4, and shows interesting short hydrogen-bonding interactions that include the formation of hydroxonium species.

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....

Plane-Wave Density Functional Theory Meets Molecular Crystals: Thermal Ellipsoids and Intermolecular Interactions.

Molecular compounds, organic and inorganic, crystallize in diverse and complex structures. They continue to inspire synthetic efforts and "crystal engineering", with implications ranging from fundamental questions to pharmaceutical research. The structural complexity of molecular solids is linked with diverse intermolecular interactions: hydrogen bonding with all its facets, halogen bonding, and other secondary bonding mechanisms of recent interest (and debate). Today, high-resolution diffraction experiments allow unprecedented insight into the structures of molecular crystals. Despite their usefulness, however, these experiments also face problems: hydrogen atoms are challenging to locate, and thermal effects may complicate matters. Moreover, even if the structure of a crystal is precisely known, this does not yet reveal the nature and strength of the intermolecular forces that hold it together. In this Account, we show that periodic plane-wave-based density functional theory (DFT) can be a useful, and sometimes unexpected, complement to molecular crystallography. Initially developed in the solid-state physics communities to treat inorganic solids, periodic DFT can be applied to molecular crystals just as well: theoretical structural optimizations "help out" by accurately localizing the elusive hydrogen atoms, reaching neutron-diffraction quality with much less expensive measurement equipment. In addition, phonon computations, again developed by physicists, can quantify the thermal motion of atoms and thus predict anisotropic displacement parameters and ORTEP ellipsoids "from scratch". But the synergy between experiment and theory goes much further than that. Once a structure has been accurately determined, computations give new and detailed insights into the aforementioned intermolecular interactions. For example, it has been debated whether short hydrogen bonds in solids have covalent character, and we have added a new twist to this discussion using an orbital-based theory that once more had been developed for inorganic solids. However, there is more to a crystal structure than a handful of short contacts between neighboring residues. We hence have used dimensionally resolved analyses to dissect crystalline networks in a systematic fashion, one spatial direction at a time. Initially applied to hydrogen bonding, these techniques can be seamlessly extended to halogen, chalcogen, and pnictogen bonding, quantifying bond strength and cooperativity in truly infinite networks. Finally, these methods promise to be useful for (bio)polymers, as we have recently exemplified for α-chitin. At the interface of increasingly accurate and popular DFT methods, ever-improving crystallographic expertise, and new challenging, chemical questions, we believe that combined experimental and theoretical studies of molecular crystals are just beginning to pick up speed.

Adsorption of Nitrate and Bicarbonate on Fe-(Hydr)oxide.

In this work, we used density functional theory calculations to study the resulting complexes of adsorption and of inner- and outer-sphere adsorption-like of bicarbonate and nitrate over Fe-(hydr)oxide surfaces using acidic, neutral, and basic simulated pH conditions. High-spin states that follow the 5N + 1 (N is the number of Fe atoms, each having five unpaired electrons) rule are preferred. Monodentate mononuclear (MM1) surface complexes are shown to lead to the most favorable thermodynamic adsorption for both bicarbonate and nitrate with -63.91 and -28.25 kJ/mol, respectively, under neutral conditions. Our results suggest that four types of regular and charged-assisted hydrogen bonds are involved in the adsorption process; all of them can be classified as closed-shell (long-range or ionic). The formal charges induce unusually short and strong hydrogen bonds. The ability of high multiplicity states of Fe clusters to adsorb oxyanions in solvated environments arises from orbital interactions: the 4s virtual orbitals in Fe have a large affinity for the 2p-type electron pairs of oxygens.

Hydrothermal and ionothermal synthesis of mineral-related arsenates in the system CdO–MO– As2 O5 (M 2+= Mg, Co, Ni, Cu, Zn) and their crystal structures

During systematic research on the mineral-related arsenates in the system CdO– M O–As 2 O 5 –H 2 O ( M 2+ = Mg, Co, Ni, Cu, Zn), three new Cd-containing arsenates Cd 4.65 Ni 0.35 (AsO 4 ) 2 (HAsO 4 ) 2 ·4H 2 O ( 1 ), Cd 0.75 Co 2.75 (H 0.5 AsO 4 ) 2 (HAsO 4 ) ( 2 ) and Cd 1.25 Zn 0.75 (HAsO 4 ) 2 ·2H 2 O ( 3 ) have been synthesized under hydrothermal conditions, while the Zn-arsenate Zn 9 (AsO 4 ) 6 ·4H 2 O ( 4 ) and again 2 have been prepared under ionothermal conditions using the ionic liquid 1-ethyl-3-methylimidazolium bromide, (C 6 H 11 N 2 )Br, as the solvent. Their crystal structures were determined using single-crystal X-ray diffraction data and refined to the reasonably low R -values: 1 – R 1 = 0.030; 2 – R 1 = 0.047; 3 – R 1 = 0.029; 6 – R 1 = 0.029. The compounds 1 , 2 and 3 are structural analogues of three different arsenate mineral phases. Compound 4 was for the first time synthesized using ionic liquid as the solvent and the hydrogen atoms were found and refined. Infrared and Raman spectra were measured and evaluated in order to obtain further information on the anion groups and especially on the short hydrogen bonds. The OH stretching frequency is in good agreement with the observed O … O distances. The different approaches in the synthesis of mineral-related arsenates, the temperature treatment as well as the role of added water in ionothermal synthesis are also discussed.

Structural and vibrational characterization of anhydrous and dihydrated species of trehalose based on the FTIR and FTRaman spectra and DFT calculations

In this study, three anhydrous species of trehalose and their dihydrated form were studied using the Fourier Transform Infrared (FTIR) and Raman spectroscopy combined with theoretical calculations derived from the theory of the functional of the density (DFT). Here, the structural and vibrational properties were predicted using the hybrid B3LYP/6-31G∗ method. The complete vibrational assignments were performed using the scaled mechanical force fields (SQMFF) methodology and their internal normal coordinates. The natural bond orbital (NBO) and atoms in molecules (AIM) calculations predicted high stabilities for the dihydrated species in gas and aqueous solution phases. The little variation observed in the dipole moment for the dihydrated species in solution could be related to a small perturbation of water hydration shell and short hydrogen bonds, as revealed by NBO and AIM studies. The lower volume expansion, low solvation energy and the higher nucleophilicity index observed for trehalose species in solution, in relation to maltose and sucrose could probably explain that different water molecules are around of trehalose/water mixtures generating higher “rigidity” in trehalose, as was experimentally reported in the literature. On the other hand, the low f(νO–H)H2O force constant value for trehalose, as compared with maltose and lactose could justify the very fragile character from the trehalose/water system to the temperature and concentration changes, as was experimentally observed from viscosity and Raman scattering studies.

Short Carboxylic Acid-Carboxylate Hydrogen Bonds Can Have Fully Localized Protons.

Short hydrogen bonds (H-bonds) have been proposed to play key functional roles in several proteins. The location of the proton in short H-bonds is of central importance, as proton delocalization is a defining feature of low-barrier hydrogen bonds (LBHBs). Experimentally determining proton location in H-bonds is challenging. Here, bond length analysis of atomic (1.15-0.98 Å) resolution X-ray crystal structures of the human protein DJ-1 and its bacterial homologue, YajL, was used to determine the protonation states of H-bonded carboxylic acids. DJ-1 contains a buried, dimer-spanning 2.49 Å H-bond between Glu15 and Asp24 that satisfies standard donor-acceptor distance criteria for a LBHB. Bond length analysis indicates that the proton is localized on Asp24, excluding a LBHB at this location. However, similar analysis of the Escherichia coli homologue YajL shows both residues may be protonated at the H-bonded oxygen atoms, potentially consistent with a LBHB. A Protein Data Bank-wide screen identifies candidate carboxylic acid H-bonds in approximately 14% of proteins, which are typically short [⟨dO-O⟩ = 2.542(2) Å]. Chemically similar H-bonds between hydroxylated residues (Ser/Thr/Tyr) and carboxylates show a trend of lengthening O-O distance with increasing H-bond donor pKa. This trend suggests that conventional electronic effects provide an adequate explanation for short, charge-assisted carboxylic acid-carboxylate H-bonds in proteins, without the need to invoke LBHBs in general. This study demonstrates that bond length analysis of atomic resolution X-ray crystal structures provides a useful experimental test of certain candidate LBHBs.

Synthesis, Structure, and Magnetic Properties of New Spin Crossover Fe(II) Complexes Forming Short Hydrogen Bonds with Substituted Dicarboxylic Acids

We synthesized new Fe(II) compounds consisting of [Fe(L)2] (HL: 2-Acetylpyridine isonicotinoylhydrazone) and dicarboxylic acids. Single crystal analysis shows that short hydrogen bonds are formed between [Fe(L)2] and dicarboxylic acids. The hydrogen bonding interactions between metal complexes and dicarboxylic acids are complemented by π-π interactions, forming two-dimensional network structures. Magnetic properties show that the Fe(II) compounds exhibit gradual spin crossover behavior around room temperature and a T1/2 value is dependent on the halogen substituent on the dicarboxylic acids.

A cadaveric study on the variant branching pattern of internal iliac artery

The molecular structure of 1:2:1 adduct of diprotonated 1,4-diazabicyclo[2.2.2]octane, (DABCO), hydrogen squarates (HSQ−) and water (1) has been characterized by single-crystal X-ray diffraction and infrared spectroscopy. The crystals of 1 are orthorhombic, space group Pnma. The non-equivalent HSQ− anions are bonded into zigzag chains (α-chain) by two short OH⋯O hydrogen bonds of 2.485(2) and 2.509(2) Å, and additionally H-bonded by water molecules linking the zigzag chains into ribbons. The diprotonated DABCO cations are located between the ribbons and interact with HSQ− anions by the NH⋯O trifurcated hydrogen bonds. The FTIR spectrum shows a very broad absorption in the 1740–550 cm−1 region, typical of short hydrogen bonds and it is attributed to the ν(OHO) and γ(OHO) vibrations. The second derivative spectrum distinguishes the νCO and γCC modes assigned to the π-delocalized squaric acid ring.

Hydrogen maleate salts: precise and accurate determination of the hydrogen atom position in short hydrogen bonds using X-ray diffraction at extremely low temperatures

Hydrogen maleate salts: precise and accurate determination of the hydrogen atom position in short hydrogen bonds using X-ray diffraction at extremely low temperatures

Theoretical study of the hydrolysis of HOSO+NO2 as a source of atmospheric HONO: effects of H2O or NH3

Environmental contextNitrous acid (HONO) has long been recognized as an important atmospheric pollutant, with the reaction of HOSO+NO2 being a source of HONO. We explore the effects of an additional water or ammonia molecule on this reaction. Calculations show that the ammonia molecule has a more effective role than the water molecule in assisting the reaction. AbstractDepending on different ways that NO2 approaches the HOSO radical, the main reactant complexes HOS(O)NO2 and HOS(O)ONO–L (lowest energy structure of the isomer) were revealed by Lesar et al. (J. Phys. Chem. A 2011, 115, 11008), and the reaction of HOSO+NO2 is a source of trans (t)-HONO and SO2. In the present work, the water molecule in the hydrolysis reaction of HOSO+NO2 not only acts as a catalyst giving the products of t-HONO+SO2, but also as a reactant giving the products of t-HONO+H2SO3, c-HONO+H2SO3 and HNO3+t-S(OH)2. For the reaction of HOSO+NO2+H2O, the main reaction paths 2, 7, and 9 are further investigated with an additional water or ammonia molecule. The CBS-QB3 calculation result shows that the process of HOS(O)NO2–H2O → t-HONO–SO2–H2O is favourable with a barrier of 0.1kcal mol–1. Although the following process of t-HONO–SO2–H2O → t-HONO–H2SO3 is unfavourable with a barrier 33.6kcal mol–1, the barrier is reduced by 17.3 or 26.3kcal mol–1 with an additional water or ammonia molecule. Starting with HOS(O)ONO–L–H2O, the energy barriers of path 7 and path 9 are reduced by 8.9 and 8.5kcal mol–1 with an additional water molecule and by 9.9 and 9.2kcal mol–1 with an additional ammonia molecule. Ammonia is more beneficial than water for assisting the HOSO+NO2+H2O reaction. Three t-HONO–H2SO3 isomers which contain double intermolecular hydrogen bonds are studied by frequency and natural bond orbital calculations. Frequency calculations show that all hydrogen bonds exhibit an obvious red shift. The larger second-order stabilisation energies are consistent with the shorter hydrogen bonds. H2SO3 can promote the process of t-HONO → HNO2, and reduce the barrier by 45.2kcal mol–1. The product NH3–H2SO3 can further form a larger cluster (NH3–H2SO3)n (n=2, 4) including NH4+HSO3– ion pairs.

Inverse Ubbelohde effect in the short hydrogen bond of photosystem II: Relation between H/D isotope effect and symmetry in potential energy profile.

The short hydrogen bond between tyrosine Yz and D1-His190 of photosystem II (PSII) was investigated using multicomponent quantum mechanics, where the quantum fluctuation of a hydrogen nucleus was incorporated into electronic structure calculation. Our computation demonstrated that the deuteration for hydrogen in the short hydrogen bond of PSII led to the reduction of the O…N distance. It indicated an inverse Ubbelohde effect typically recognized in strong and symmetric hydrogen-bonding clusters such as FHF(-) and H3O2-. We confirmed that the relation between the geometric isotope effect and the symmetry of the potential energy profile of FHF(-) was reasonably agreed with that of PSII. According to this agreement, the short hydrogen bond in PSII can be regarded as a short strong hydrogen bond. © 2016 Wiley Periodicals, Inc.