Short Hydrogen Bond Research Articles

The relation between Li Na substitution and hydrogen bonding in five-periodic single-chain silicates nambulite and marsturite: A single-crystal X-ray study

Isomorphic nambulite, natronambulite, marsturite, and lithiomarsturite belong to the p-p (pectolitepyroxene) series of pyroxenoid group minerals with five-periodic single chains of tetrahedra and the common simplified composition (Li,Na)(Mn,Ca) 4 [Si 5 O 14 (OH)] (Z = 2, space group P1̄). New crystal structure refinements including localization of H positions of four samples (two nambulite, one natronambulite, and one marsturite) with varying Li and Na concentrations and major to trace element compositional data from different localities are presented. Na occupies a strongly distorted eightfoldcoordinated site (M5). Li replacing Na has a substantially smaller ionic radius and occupies a pocket of the large M5 coordination polyhedron and is only fivefold coordinated by oxygen. Thus, the Li ↔ Na substitution has a significant influence on the bond-valence sums of oxygen sites forming the large cage around M5. Two of the cage-building oxygen sites (O1 and O11) are involved in hydrogen bonding. If M5 is occupied by Na or empty as in the closely related babingtonite, Ca 2 Fe 2 [Si 5 O 14 (OH)], the OH-group is at O1 and exhibits a strong hydrogen bond to O11. If a pocket of M5 is occupied by Li, the hydrogen bond system is reversed with OH at O11 and a strong hydrogen bond to O1. This study emphasizes that short hydrogen bonds with O-H···O separations of ca. 2.46 Å may be modified by homovalent substitution, which contributes to the understanding of strong hydrogen bonds and their role in the stability of hydrous pyroxenoids with strongly curled silicate chains.

(μ-Di-hydrogen pyrazine-2,3,5,6-tetra-carboxyl-ato-κ(6) O (2),N (1),O (6);O (3),N (4),O (5))bis-(di-aqua-lithium) monohydrate.

The structure of the title compound, [Li2(C8H2N2O8)(H2O)4]·H2O, is composed of dinuclear mol­ecules in which the ligand bridges two symmetry-related LiI ions, each coordinated also by two water O atoms, in an O,N,O′-manner. The Li and N atoms occupy special positions on twofold rotation axes, whereas a crystal water mol­ecule is located at the inter­section of three twofold rotation axes. The LiI cation shows a distorted trigonal–bipyramidal coordination. Two carboxyl­ate groups remain protonated and form short inter­ligand hydrogen bonds. The mol­ecules are held together by a network of hydrogen bonds in which the coordinating and solvation water mol­ecules act as donors and carboxyl­ate O atoms as acceptors, forming a three-dimensional architecture.

Cooperativity Assisted Shortening of Hydrogen Bonds in Crystalline Oxalic Acid Dihydrate: DFT and NBO Model Studies.

The distance of ∼2.49 Å separating the carboxylic OH oxygen from the water oxygen atom in the α-polymorph of crystalline oxalic acid dihydrate is by ∼0.1 Å shorter than the average distance in carboxylic acid monohydrates. It is also by ∼0.2 Å shorter than the corresponding distance presently calculated for the heterotrimer consisting of one acid and two water molecules. The large difference between RO···O in the heterotrimer and in the crystal is attributed to the cooperative effect in the latter; this is supported by calculations carried out on clusters constituted of an increasing number of acid and water molecules. The present DFT calculations with geometry optimization include seven isolated model clusters, the largest of which contains five acid and eight water molecules. The RO···O of the short hydrogen bond shortens progressively with increasing the number of cluster constituents; in the largest cluster, it reaches 2.50 Å. This is remarkably close to both the experimental distance as well as to the distance obtained by the periodic DFT calculation. The electronic effects were studied by Natural Bond Orbital analysis, revealing an enhancement of hydrogen bonding on extending the network by increased polarization of the carbonyl group and by the increased delocalization interaction between the lone electron pair on the acceptor oxygen atom and the OH antibond orbital. The formation of circular motifs appears to be the most important factor in the cooperative shortening of the hydrogen bonds. In agreement with the measured hydrogen bond distances, inspection of the electron density reveals a notable difference in hydrogen bond shrinking tendency between the two known polymorphs of the title system.

Can quantum-chemical NMR chemical shifts be used as criterion for force-field development.

Fragment-based quantum chemical calculations based on our adjustable density matrix assembler (ADMA) are able to calculate NMR chemical shifts even for proteins and protein-protein complexes [1,2]. The agreement between the calculated and experimental chemical shifts in these calculations is, however, highly dependent on including conformational sampling and explicit solvent molecules. On the one hand, ensembles taken from classical MD simulations are suited for 13C and 1H chemical shift calculations if polar protons are neglected [3]. On the other hand, input structures from a Car–Parrinello MD resulted in landmark improvements over calculations based on classical MD especially for amide protons, which are predicted too high-field shifted based on the latter ensembles [4]. The better results are caused by the solute–solvents interactions forming shorter hydrogen bonds as well as by the internal degrees of freedom of the solute. With the obtained accuracy and the possibility of identifying the structural reasons for discrepancies between the experimental and calculated data, NMR chemical-shift calculations are now a perfect tool for e.g. the validation of new, improved force fields.

The structure of an authentic spore photoproduct lesion in DNA suggests a basis for recognition.

The spore photoproduct lesion (SP; 5-thymine-5,6-dihydrothymine) is the dominant photoproduct found in UV-irradiated spores of some bacteria such as Bacillus subtilis. Upon spore germination, this lesion is repaired in a light-independent manner by a specific repair enzyme: the spore photoproduct lyase (SP lyase). In this work, a host-guest approach in which the N-terminal fragment of Moloney murine leukemia virus reverse transcriptase (MMLV RT) serves as the host and DNA as the guest was used to determine the crystal structures of complexes including 16 bp oligonucleotides with and without the SP lesion at 2.14 and 1.72 Å resolution, respectively. In contrast to other types of thymine-thymine lesions, the SP lesion retains normal Watson-Crick hydrogen bonding to the adenine bases of the complementary strand, with shorter hydrogen bonds than found in the structure of the undamaged DNA. However, the lesion induces structural changes in the local conformation of what is otherwise B-form DNA. The region surrounding the lesion differs significantly in helical form from B-DNA, and the minor groove is widened by almost 3 Å compared with that of the undamaged DNA. Thus, these unusual structural features associated with SP lesions may provide a basis for recognition by the SP lyase.

Structural evidence of an intramolecular proton transfer leading to keto-amine tautomer in the crystals of Schiff bases derived from tyrosine and histidine esters

Three Schiff bases derived from of 2,4-dihydroxybenzaldehyde or 2,4-dihydroxyacetophenone and esters of tyrosine and histidine have been synthesized and the crystal and molecular structures determined by single crystal X-ray diffraction. The molecular structures of the three compounds are dominated by short intramolecular hydrogen bonds with distances N⋯O ranging from 2.536(2) to 2.588(2)Å and the hydrogen atom is bonded to the nitrogen. In the solid state, the structures are characterized by the keto-amine tautomer, whereas in the solution the phenol-imine form was detected by 1H NMR spectroscopy. Intermolecular interactions influencing crystal packing are discussed.

Hydrogen bonding and proton transfer in cocrystals of 4,4'-bipyridyl and organic acids studied using nuclear quadrupole resonance.

Cocrystals of 4,4'-bipyridyl and several carboxylic acids were grown from the methanol solution of the cocrystal formers. Complete (14)N NQR spectra of these cocrystals have been measured using (1)H-(14)N nuclear quadrupole double resonance. The principal values of the quadrupole coupling tensor are calculated from the (14)N NQR frequencies. A large variation in the (14)N quadrupole coupling constant between 1.3 MHz and 4.7 MHz is observed. A very low (14)N quadrupole coupling constant, characteristic for proton transfer O-H···N → O(-)···H-N(+), is observed in 4,4'-bipyridyl-oxalic acid (1 : 1). In 4,4'-bipyridyl-5-chlorosalycilic acid (1 : 1) the (14)N NQR data show the presence of a short, strong N···H···O hydrogen bond. A correlation of the principal values of the (14)N quadrupole coupling tensor is observed. The correlation is analyzed in the model, where the deformation of the lone pair electron orbital and the change of the population of the π-electron orbital produce the variation of the (14)N quadrupole coupling tensor in the hydrogen bonded 4,4'-bipyridyl. The temperature variation of the (14)N quadrupole coupling tensor in 4,4'-bipyridyl-5-chlorosalycilic acid (1 : 1) is analyzed. Proton displacement within the N···H···O hydrogen bond and the change of the population of the π-electron orbital at the two nitrogen positions in a 4,4'-bipyridyl molecule in the temperature interval between 157 K and 323 K are determined.

Living on acetylene. A primordial energy source.

The tungsten iron-sulfur enzyme acetylene hydratase catalyzes the conversion of acetylene to acetaldehyde by addition of one water molecule to the C-C triple bond. For a member of the dimethylsulfoxide (DMSO) reductase family this is a rather unique reaction, since it does not involve a net electron transfer. The acetylene hydratase from the strictly anaerobic bacterium Pelobacter acetylenicus is so far the only known and characterized acetylene hydratase. With a crystal structure solved at 1.26 Å resolution and several amino acids around the active site exchanged by site-directed mutagenesis, many key features have been explored to understand the function of this novel tungsten enzyme. However, the exact reaction mechanism remains unsolved. Trapped in the reduced W(IV) state, the active site consists of an octahedrally coordinated tungsten ion with a tightly bound water molecule. An aspartate residue in close proximity, forming a short hydrogen bond to the water molecule, was shown to be essential for enzyme activity. The arrangement is completed by a small hydrophobic pocket at the end of an access funnel that is distinct from all other enzymes of the DMSO reductase family.

Car-Parrinello and path integral molecular dynamics study of the intramolecular hydrogen bonds in the crystals of benzoylacetone and dideuterobenzoylacetone.

The dynamics of the intramolecular short hydrogen bond in the molecular crystal of benzoylacetone and its deuterated analogue are investigated using ab initio molecular dynamics simulations. A study on intramolecular hydrogen bonding in 1-phenyl-1,3-butadione (I) and 1-deuteroxy-2-deutero-1-phenylbut-1-en-3-one (II) crystals has been carried out at 160 K and 300 K on the CPMD method level and at 300 K on the PIMD method level. The analysis of the two-dimensional free-energy landscape of reaction coordinate δ-parameter and ROO distances shows that the hydrogen (deuter) between the two oxygen atoms adopts a slightly asymmetrical position in the single potential well. When the nuclear quantum effects are taken into account, very large delocalization of the bridging proton is observed. These studies indicate that hydrogen bonds in the crystal of benzoylacetone have characteristic properties for the type of bonding model resonance-assisted hydrogen bonds (RAHB) without existing the equilibrium of the two tautomers. The infrared spectrum has been calculated, and a comparative vibrational analysis has been performed. The CPMD vibrational results appear to qualitatively agree with the experimental ones.

Furosemide Cocrystals: Structures, Hydrogen Bonding, and Implications for Properties

In this paper, we report the crystal growth of four cocrystals of furosemide (4-chloro-2-[(2-furanylmethyl)amino]-5-sulfamoylbenzoic acid), a loop diuretic drug used for the treatment of hypertension and edemas, prepared with p-aminobenzoic acid, nicotinamide, and isonicotinamide as coformers. We present four new crystal structures and elucidate the intermolecular interactions present in the cocrystals. The structures display interesting supramolecular chemistry: a number of different synthons, as well as short strong hydrogen bonds with partial proton transfer and indications of proton disorder. Using powder X-ray diffraction, solid state NMR, and thermal analysis, we provide evidence for the preparation of bulk samples of two compositions, namely, the 1:1 cocrystal of furosemide and p-aminobenzoic acid and 2:1 cocrystal of furosemide and isonicotinamide, highlighting the general necessity of such multitechnique approaches to characterize organic solids (including cocrystals and solvates) prepared by gri...

Synthesis, crystal structure and infrared and Raman spectra of a sodium barium orthoarsenate (V) nonahydrate NaBaAsO4(H2O)9

Crystals of a sodium barium orthoarsenate (V) nonahydrate were synthesized by slow evaporation from aqueous solutions. The crystal structure was solved and refined by single-crystal X-ray diffraction. The crystal is cubic, space group P213, a=10.838(2)Å; Z=4 and V=1273.1(2)Å3. Its structure is composed of BaO9 and NaO6 polyhedra and AsO4 tetrahedral units. The short hydrogen bond length O4H42⋯O2B of 2.496Å was confirmed by infrared spectroscopy. In addition, Raman spectrum was recorded in order to study the arsenate group and the cation motion (lattice modes) in the title compound.

Structural insights into the function of a thermostable copper-containing nitrite reductase

Copper-containing nitrite reductase (CuNIR) catalyzes the reduction of nitrite (NO(-)2) to nitric oxide (NO) during denitrification. We determined the crystal structures of CuNIR from thermophilic gram-positive bacterium, Geobacillus thermodenitrificans (GtNIR) in chloride- and formate-bound forms of wild type at 1.15 Å resolution and the nitrite-bound form of the C135A mutant at 1.90 Å resolution. The structure of C135A with nitrite displays a unique η(1)-O coordination mode of nitrite at the catalytic copper site (T2Cu), which has never been observed at the T2Cu site in known wild-type CuNIRs, because the mobility of two residues essential to catalytic activity, Asp98 and His244, are sterically restricted in GtNIR by Phe109 on a characteristic loop structure that is found above Asp98 and by an unusually short CH-O hydrogen bond observed between His244 and water, respectively. A detailed comparison of the WT structure with the nitrite-bound C135A structure implies the replacement of hydrogen-bond networks around His244 and predicts the flow path of protons consumed by nitrite reduction. On the basis of these observations, the reaction mechanism of GtNIR through the η(1)-O coordination manner is proposed.

New chemical analogs of triglycine sulfate

Triglycine sulfate (TGS) and its analogs can be presented by the molecular structure AH(A⋯AH)Y, where A is an amino acid (glycine in TGS) in zwitter-ionic form, AH is a protonated cationic amino acid, (A⋯AH) is a dimeric cation, where A and AH are connected by a short hydrogen bond, and Y is a divalent anion. Doing research on amino acid hexafluorosilicates we obtained a series of salts with different compositions, including four hexafluorosilicate salts which chemically are analogs of triglycine sulfate. Those are GlyH(Gly⋯GlyH)SiF6 (I), SarH(Sar⋯SarH)SiF6·2H2O (II), l-AlaH(l-Ala⋯l-AlaH)SiF6·H2O (III) and l-ProH(l-Pro⋯l-ProH)SiF6·H2O (IV). We have already published our results on crystals (II) and (III). In this work we report our results on the crystals (I) and (IV).

Short hydrogen bonds in 2,4-dinitrobenzoic acid complexed with pyridine

The aim of this work was to describe the vibrations connected with the short hydrogen bonds of differing geometries in 2,4-dinitrobenzoic acid and in 2,4-dinitrobenzoic acid complexed in two ratios with pyridine. All three compounds contain short hydrogen bonds either between two acid molecules (OH⋯O bond) or between acid and pyridine (NH⋯O bonds) or both. We selectively deuterated the proton of the 2,4-dinitrobenzoic acid molecule involved in the proton transfer to aid in the assignment of the H-bond protonic modes. The compounds have been characterized with single crystal X-ray diffraction, CHN elemental analysis, FT-IR and IINS spectroscopy. We show that our combination of analytical methods with DFT calculations represents a fruitful approach to observe the relationship between the geometries of hydrogen bonds and their dynamics.

Molecular mobility of imidazoles in molten state as a key factor to enhance proton conductivity

A systematic study on alkyl urocanates related to the proton conductivity performances to clarify the role of molecular mobility and hydrogen bond in proton transfer is carried out. Depending on the methylene units, the melting (Tm) and degradation temperatures (Td) change remarkably. When methylene unit is four, C4U shows the lowest melting point (as low as 46 °C) and this suggests the favorable molecular mobility in the molten state. The short hydrogen bond distance and the short T1 relaxation time lead to a scheme of proton conductivity of C4U to be under a regular imidazole arrangement with highly active alkyl chain molecular motion. When C4U is in molten state, the proton transfer is under vehicle mechanism clarified by Volgel–Tammann–Fulcher (VTF) equation. By applying C4U as a proton conductive additive in a sulfonated poly(ether ether ketone) (SPEEK) membrane without any acid dopants, the proton conductivity in the heating process up to 170 °C continuously increases to be ∼104 times higher than that of the neat SPEEK. The present work not only demonstrates the thermal mobility as a key factor to govern the proton conductivity but also proposes the effective proton transfer of heterocyclic compounds based on the molten state.

Relations between structure and physicooptical properties of Eu3+ and Tb3+ tetraphosphonates

The crystal structure of the Tb3+ complex with ethylenediaminetetra(methylenephosphonic acid) (H8EDTMP) was determined and it was found that the compound is isostructural with the previously studied [C(NH2)3]7[Eu(EDTMP)(CO3)]⋅10H2O crystal. The Eu3+ and Tb3+ complexes with trans-cyclohexane-1,2-diamine-N,N,N′,N′-tetrakis(methylenephosphonic acid) (H8CDTMP) of known crystal structures were also obtained. As it results from the X-ray analyses both tetraphosphonate ligands (EDTMP and CDTMP) bind the Ln3+ ion with 2 nitrogen atoms and 4 oxygen atoms in such a way that only one oxygen atom from each phosphonate group is linked with the central ion. The coordination sphere is completed by two oxygen atoms of the bidendate carbonate anion in the case of Ln3+–EDTMP complexes, whereas two monomeric Ln3+–CDTMP complex anions are connected by two hydroxyl ions and one water molecule. The spectroscopic (FTIR and emission) studies of crystals are presented and discussed with respect to their structures. It was shown that OH oscillators present in the inner-sphere of Eu3+ and Tb3+ complexes with CDTMP do not quench lanthanide emission. The reasons of that are three very short hydrogen bonds (∼2Å) formed between two hydroxyl groups and a water molecule. The luminescence lifetimes and quantum yields of lanthanide tetraphosphonates were compared with those obtained for Ln3+ tetracarboxylates.

Dissociative Photoionization of Glycerol and its Dimer Occurs Predominantly via a Ternary Hydrogen-Bridged Ion–Molecule Complex

The photoionization and dissociative photoionization of glycerol are studied experimentally and theoretically. Time-of-flight mass spectrometry combined with vacuum ultraviolet synchrotron radiation ranging from 8 to 15 eV is used to investigate the nature of the major fragments and their corresponding appearance energies. Deuterium (1,1,2,3,3-D5) and (13)C (2-(13)C) labeling is employed to narrow down the possible dissociation mechanisms leading to the major fragment ions (C3H(x)O2(+), C2H(x)O2(+), C2H(x)O(+), CH(x)O(+)). We find that the primary fragmentation of the glycerol radical cation (m/z 92) occurs only via two routes. The first channel proceeds via a six-membered hydrogen-transfer transition state, leading to a common stable ternary intermediate, comprised of neutral water, neutral formaldehyde, and a vinyl alcohol radical cation, which exhibits a binding energy of ≈42 kcal/mol and a very short (1.4 Å) hydrogen bond. Fragmentation of this intermediate gives rise to experimentally observed m/z 74, 62, 44, and 45. Fragments m/z 74 and 62 both consist of hydrogen-bridged ion-molecule complexes with binding energy >25 kcal/mol, whereas the m/z 44 species lacks such stabilization. This explains why water- or formaldehyde-loss products are observed first. The second primary fragmentation route arises from cleaving the elongated C-C bond. Also for this channel, intermediates comprised of hydrogen-bridged ion-molecule complexes exhibiting binding energies >24 kcal/mol are observed. Energy decomposition analysis reveals that electrostatic and charge-transfer interactions are equally important in hydrogen-bridged ion-molecule complexes. Furthermore, the dissociative photoionization of the glycerol dimer is investigated and compared to the main pathways for the monomeric species. To a first approximation, the glycerol dimer radical cation can be described as a monomeric glycerol radical cation in the presence of a spectator glycerol, thus giving rise to a dissociation pattern similar to that of the monomer.

Švenekite, Ca[AsO2(OH)2]2, a new mineral from Jáchymov, Czech Republic

AbstractŠvenekite (IMA 99-007), Ca[AsO2(OH)2]2, is a rare supergene arsenate mineral occurring in the Geschieber vein, Jáchymov ore district, Western Bohemia, Czech Republic. It grows directly on the granite rocks and occurs isolated from other arsenate minerals otherwise common in Jáchymov. Švenekite usually forms clear transparent coatings composed of indistinct radiating to rosette-shaped aggregates up to 3 mm across. They are composed of thin lens- or bladed-shaped crystals, usually 100 – 150 μm long. Švenekite is transparent to translucent and has a white streak and a vitreous lustre; it does not fluoresce under ultraviolet light. Cleavage is very good on {010}. The Mohs hardness is ∼2. Švenekite is biaxial, non-pleochroic. The refractive indices are α' = 1.602(2), γ' = 1.658(2). The empirical formula of švenekite (based on As + P + S = 2 a.p.f.u., an average of 10 spot analyses) is (Ca1.00Mg0.01)Σ1.01[AsO2(OH)2]1.96[PO2(OH)2]0.03(SO4)0.01. The simplified formula is Ca[AsO2(OH)2]2 and requires CaO 17.42, As2O571.39, H2O 11.19, total 100.00 wt.%. Raman and infrared spectroscopy exhibit dominance of O – H vibrations and vibration modes of distorted tetrahedral AsO2(OH)2 units. Švenekite is triclinic, space group P, with a = 8.5606(5), b = 7.6926(6), c = 5.7206(4) Å, α = 92.605(6), β = 109.9002(6), γ = 109.9017(6)º, and V = 327.48(4) Å3, Z = 2, Dcalc = 3.26 g·cm–3. The a:b:c ratio is 0.7436:1:1.1082 (for single-crystal data). The six strongest diffraction peaks in the X-ray powder diffraction pattern are [d (Å)/I(%)/(hkl)]: 3.968(33)(20); 3.766(35)(2); 3.697(49)(101); 3.554(100)(020); 3.259(33)(20); 3.097(49)(11). The crystal structure of švenekite was refined from single-crystal X-ray diffraction data to R1 = 0.0250 based on 1309 unique observed, and to wR2 = 0.0588, for all 1588 unique reflections (with GOFall = 1.20). The structure of švenekite consists of sheets of corner-sharing CaO8 polyhedra and AsO2 OH2 groups, stacked parallel to (001). Adjacent sheets are linked by hydrogen bonds. The švenekite structure possesses very short symmetrical hydrogen bonds (with the D–H lengths ∼1.22 Å). The mineral is named to honour Jaroslav Švenek, the former curator of the mineralogical collection of the National Museum in Prague, Czech Republic.

AAAA-DDDD Quadruple Hydrogen-Bond Arrays Featuring NH···N and CH···N Hydrogen Bonds

The X-ray crystal structure of a previously reported extremely strong quadruple NH···N AAAA-DDDD hydrogen-bond array [5·4] (K(a) = 1.5 × 10(6) M(-1) in CH3CN; K(a) > 3 × 10(12) M(-1) in CH2Cl2) features four short linear hydrogen bonds. Changing the two benzimidazole groups of the DDDD unit to triazole groups replaces two of the NH···N hydrogen bonds with CH···N interactions (complex [5·6]), but only reduces the association constant in CH3CN by 2 orders of magnitude (K(a) = 2.6 × 10(4) M(-1) in CH3CN; K(a) > 1 × 10(7) M(-1) in CH2Cl2). Related complexes without the triazole groups range in K(a) from 18 to 270 M(-1) in CH3CN, suggesting that the CH···N interactions can be considered part of a strong AAAA-DDDD quadruple hydrogen-bonding array. The NH···N/CH···N AAAA-DDDD motif can be repeatedly switched "on" and "off" in CDCl3 through successive additions of acid and base.

Investigations of the Very Short Hydrogen Bond in the Crystal of Nitromalonamide via Car–Parrinello and Path Integral Molecular Dynamics

In this paper are presented the results of theoretical studies of the structure in proton motion in a very short O···O and two weak N-H···O intramolecular hydrogen bonds in the nitromalonamide crystal. The dynamics of proton motion in hydrogen bonds were investigated in the NVT ensemble at 298 K using the Car-Parrinello and the path integral molecular dynamics. A very large delocalization of proton in the slightly asymmetrical single well of free energy potential of O-H···O intramolecular hydrogen bond was noted especially in the path integral simulation where quantum effects are taken into account. This hydrogen bond is very strong with the estimated energy of hydrogen bond ca. -27 kcal/mol. The nature of intra- and intermolecular interactions was studied by means of quantum theory of atoms in molecules. The infrared spectra were calculated and compared with available experimental data. CPMD vibrational results appear to be in good agreement with the experimental ones.