OP Hydrogen Bonds Research Articles

Caesium propano-ate monohydrate.

Caesium propano-ate monohydrate, Cs+·C3H5O2 -·H2O, is composed of two symmetry-independent Cs+ cations, which are situated on the special position 4e of space group P 21 m, one symmetry-independent propano-ate mol-ecule in a general position and a pair of water mol-ecules also situated on special position 4e. Two pairs of these symmetry-independent cations, four propano-ate mol-ecules and two pairs of symmetry-independent water mol-ecules form a repeat unit. These units form columns that are directed along the c axis and possess symmetry mm2. There are four such columns passing through each unit cell. Each column is inter-connected to its neighbours by four bifurcated three-centred Ow-H⋯Op (w = water, p = propano-ate) hydrogen bonds of moderate strength. There are also four intra-molecular Ow-H⋯Op hydrogen bonds of moderate strength within each column. One Cs+ cation is coordinated by six oxygen atoms (two water and four carboxyl-ate) in a trigonal-prismatic geometry, while the other Cs+ cation is coordinated by four water and four carboxyl-ate O atoms in a tetra-gonal-prismatic arrangement.

Synthesis of new α-amino-1H indazolyl-phosphonate derivatives: Crystal structure, Hirshfeld surface analysis and DFT studies

A new α-amino-1H Indazolyl-phosphonates derivative 3a–e were synthesized and subjected to solid state characterization by single-crystal X-ray diffraction analysis, and to study their NMR and Hirshfeld surface analysis. The P atom exhibits tetrahedral geometry involving two O-ethyl groups, a C atom and a double-bonded O atom. The P–C bond has an approximately staggered conformation, with the aniline and substituted groups in gauche positions with respect to the PO double bond. The molecules are arranged as centrosymmetric or pseudocentrosymmetric dimers connected by two N–H⋯OP hydrogen bonds and also by C–H … π interaction in the case of structures 3a–e, which are responsible for the formation and stability of the molecular assemblies. Hirshfeld surface analysis (dnorm surface and two-dimensional (2D) fingerprint plots) revealed the nature of intermolecular contacts. The most important contributions for the crystal packing are from H⋯H, H⋯C/C⋯H, O⋯H/H⋯O, and H⋯N/N⋯H interactions. In addition, frontier molecular orbitals and Molecular Electrostatic Potential map of the compounds was produced by using the optimized structures.

Crystal structure of 4-{[(2,4-di-hydroxy-benzyl-idene)amino]-meth-yl}cyclo-hexane-carb-oxy-lic acid.

In the title compound, C15H19NO4, the cyclo­hexyl ring adopts a chair conformation with both exocyclic C—C bonds in equatorial orientations. The dihedral angle between the basal plane of cyclo­hexyl ring and the 2,4-di­hydroxy­benzaldehyde moiety is 84.13 (13)°. An intra­molecular O—H⋯N hydrogen bonds closes an S(6) ring. In the crystal, Oc—H⋯Op (c = carb­oxy­lic acid, p = phenol) hydrogen bonds link the mol­ecules into [100] C(13) chains whereas an Op—H⋯Oc hydrogen bond generates [101] C(15) chains. Together, these bonds generate (010) sheets incorporating R 2 2(20) loops. Weak C—H⋯O and C—H⋯π inter­actions also occur.

Novel organotin(IV) complexes of organophosphorus ligands: Synthesis, spectroscopic, structural study and DFT calculations

Three new phosphoric triamides with general formula C6H5C(O)NHP(O)X2, where X = N-4-phenylpiperazinyl (1), N-4-ethoxycarbonyl piperazinyl (2), and N-4-ethoxycarbonyl piperidinyl (3) as well as seven novel organotin(IV) complexes with formula SnClR1R2R3L2 where R = alkyl/aryl/Cl and L = organophosphorus ligand, were synthesized and characterized by 1H, 13C, 31P NMR, IR spectroscopy and elemental analysis. The 31P{1H} NMR spectra of compounds 9 and 10 each reveal two close signals that are related to their cis and trans isomers. DFT calculations were performed at B3LYP and M06 methods with LanL2DZ basis set using Gaussian 09 software on the cis and trans configurations of compounds 9 and 10. The structure of compound 1 was determined by X-ray crystallography. In this structure, there are two symmetrically independent molecules (1 and 1A) produced due to the co-crystallization of water and CH3OH molecules. The PO and CO bonds in both molecules 1 and 1A indicate an anti conformation relative to each other. The strong intermolecular N–H⋯OP hydrogen bonds plus weak intermolecular C–H⋯O(1W), C–H⋯OC, C–H⋯OP and C–H⋯N hydrogen bonds create a three-dimensional polymeric chain in the crystalline network.

Structural Dynamics of Bacterial Translation Initiation Factor IF2

Bacterial translation initiation factor IF2 promotes ribosomal subunit association, recruitment, and binding of fMet-tRNA to the ribosomal P-site and initiation dipeptide formation. Here, we present the solution structures of GDP-bound and apo-IF2-G2 of Bacillus stearothermophilus and provide evidence that this isolated domain binds the 50 S ribosomal subunit and hydrolyzes GTP. Differences between the free and GDP-bound structures of IF2-G2 suggest that domain reorganization within the G2-G3-C1 regions underlies the different structural requirements of IF2 during the initiation process. However, these structural signals are unlikely forwarded from IF2-G2 to the C-terminal fMet-tRNA binding domain (IF2-C2) because the connected IF2-C1 and IF2-C2 modules show completely independent mobility, indicating that the bacterial interdomain connector lacks the rigidity that was found in the archaeal IF2 homolog aIF5B.

N,N'-Dicyclo-hexyl-N'',N''-dimethyl-phospho-ric triamide.

In the title compound, C14H30N3OP, both cyclo­hexyl groups adopt chair conformations with the NH unit in an equatorial position. The P atom adopts a slightly distorted tetra­hedral environment. In the (CH3)2NP(O) unit, the O—P—N—C torsion angles, showing the orientations of the methyl groups with respect to the phosphoryl group, are −166.6 (3) and 34.6 (4)°. The O atom of the P=O group acts as a double hydrogen-bond acceptor and is involved in two different inter­molecular N—H⋯OP hydrogen bonds, building R 2 2(8) rings that are further linked into chains running parallel to the b axis.

N,N′,N′′,N′′′-Tetrakis(2-methylphenyl)oxybis(phosphonic diamide): a redetermination at 150 K with MoKα radiation

The structure of the title compound, C28H32N4O3P2, has been redetermined at 150 K, with much improved precision. The structure and mol­ecular packing of the title compound was previously determined using Cu Kα radiation, with an R value of 0.0933 [Cameron et al. (1978 ▶). Z. Naturforsch. Teil B, 33, 728–730]. The c-axis length in this structure [13.8401 (8) Å] is almost half that reported in the original study. In the title compound, two (C6H4(2-CH3)NH)2P(O) units are bridged via an O atom [P—O—P = 133.31 (11)°]. The P atoms adopt a slightly distorted tetra­hedral coordination geometry. In the crystal, mol­ecules are linked via N—H⋯OP hydrogen bonds into extended chains parallel to the c axis. An intra­molecular N—H⋯O=P hydrogen bond is also found in the mol­ecule.

1,3,5-Benzene-tri-p-phenylphosphonic Acid. A New Building Block in Supramolecular Chemistry

Benzene-1,3,5-tri-p-phenylphosphonic acid, 1,3,5-[p-C6H4P(O)(OH)2]3C6H3, (8), a novel building block for applications in supramolecular chemistry, was prepared in two steps with an overall yield of 82%. The [Pd(PPh3)4]-catalyzed Arbuzov reaction of 1,3,5-tris(p-bromophenyl)benzene with P(Oi-Pr)3 afforded benzene-1,3,5-tri-p-phenylphosphonic diisopropyl ester, 1,3,5-[p-C6H4P(O)(Oi-Pr)2]3C6H3 (9). The hydrochloric acid-catalyzed hydrolysis of 9 produced 8, which forms a crystalline salt with p-dimethylaminopyridine (DMAP) in a ratio of 2:3 (as methanol solvate) that was characterized by X-ray crystallography. The supramolecular structure features organic domains of stapled 1,3,5-triphenylbenzene units associated by PO−H···OP hydrogen bonds and π-stacking. These staples are horizontally cross-linked by PO−H···OP hydrogen bonds. The protonated DMAP molecules fill the voids between the staples and participate in the stabilization of the framework by formation of N−H···OP hydrogen bonds. The melting point of the adduct (381 °C) confirms the high thermal stability of the supramolecular framework.

Clathrate and channel inclusion systems co-exist in the crystal structure of a bis-C-pivot macrocycle (Z′ = 2)

15,22-Bis(dimethoxyphosphoryl)-2,5,8-trioxa-16,21-diazatricyclo [21.4.0.09,14] heptacosa-9,11,13,23,25,27(1)-hexaene (1c) crystallises from tetrahydrofuran/methanol (7 : 1) as an inclusion compound with one mole of each of the solvent species. The methanol occupies a clathrate inclusion site within a stacked column of host molecules, while the THF occupies channels which lie between the host columns, which are held rigidly apart by antiparallel N–H⋯OP hydrogen bonds. The marked pseudosymmetry of the crystal structure (Z′ = 2) arises because of the twisting of the host columns about their axes to reduce the channel volumes to fit THF. The phosphorylation reaction of imines used here has the potential to provide a supramolecular synthon of a predictable fixed orientation with respect to such a host molecule.

Tris(2-N-methylaminocarbonyl-3-hydroxy-1,6-dimethyl-1,4-dihydro-4-pyridinonato)iron(III) dimethylformamide disolvate

In the crystal structure of the title compound, Fe(C9H11N2O3)3·2C3H7NO, the FeIII ion is six-coordinate with a distorted octa­hedral configuration consisting of six donor O atoms from three bidentate ligands. Two of the amide NH groups are involved in intra­molecular N—H⋯Op (p = phenolic) hydrogen bonds, while the third is involved in forming centrosymmetric dimers via inter­molecular N—H⋯Op hydrogen bonds.

A tubular architecture in a phosphorus based trihydrazide, {P(S)[N(CH3)NH2]3}

The X-ray crystal structure of {P(S)[N(CH3)NH2]3} reveals a tubular architecture arising out of the N–H⋯SP hydrogen bonds while the corresponding structure of {P(O)[N(CH3)NH2]3} shows a 2-D organization mediated by the N–H⋯OP hydrogen bonds.

Vibrational Study and Crystal Structure Refinement of BaHPO4.

AbstractFor Abstract see ChemInform Abstract in Full Text.

NMR detection of intermolecular NH.OP hydrogen bonds between guanidinium protons and bisposphonate moieties in an artificial arginine receptor.

Hydrogen bonding plays a major role in the selective recognition of guanidinium groups by receptor molecules. The present NMR investigation provides direct experimental evidence of hydrogen bonds in an artificial arginine receptor complex consisting of alpha-N-benzoylarginine ethyl ester and a bisphosphonate tweezers molecule. trans-Hydrogen bond 2hJHP couplings between the phosphonate moieties and individual guanidinium protons as well as the amide proton have been detected by [1H,31P]-HMBC and [31P,1H]-INEPT experiments. The detected hydrogen bonding network in the investigated artificial arginine receptor shows a symmetrical end-on interaction of the guanidinium moiety, which enables concerted rotations and deviates from the structure proposed for the biological arginine fork.

Vibrational study and crystal structure refinement of BaHPO 4

X-ray single crystal structure of BaHPO 4 is refined in the centric space group Pbnm (No. 62) with a=4.609(1) Å, b=14.195(3) Å, c=17.214(5) Å, V=1126.3(5) Å 3, Z=12 and a final R value of 0.036 for 1261 independent reflections. The atomic arrangement consists of anionic linear chains lying parallel to the a direction and strongly linked by hydrogen bonds. Two successive chains are separated by Ba 2+ cations. A comparison of the anionic networks for some similar compounds is also given. The polarized Raman and infrared absorption spectra are investigated. A factor group analysis leads to determination of internal modes of the PO 4 3− anions. The vibrational study confirmed the strong HOP hydrogen bonds to the phosphate groups and indicated a notable hydrogen bridges in BaHPO 4 compound.

Detection of Scalar Couplings Across NH···OP and OH···OP Hydrogen Bonds in a Flavoprotein

Hydrogen bonding plays a major role in the tight binding of the FMN cofactor in flavodoxins. The present NMR investigation provides direct experimental evidence for hydrogen bonds involving the phosphate moiety of FMN in Desulfovibrio vulgaris flavodoxin. Several trans-hydrogen bond J couplings between the phosphorus nucleus and backbone amide as well as side chain hydroxyl protons of the apoprotein have been detected. It is shown that relaxation interference between 1H chemical shift anisotropy and 1H−31P dipolar interactions can also lead to correlations of these nuclei in HMBC spectra. The size of the 2hJPH coupling constants was determined using a simple 31P-detected quantitative J correlation experiment. For at least one amide group a scalar three-bond coupling between the phosphorus and nitrogen has been observed in a [15N,1H]-TROSY-type 15N−{31P} spin−echo difference experiment. With approximately 1.7 Hz its magnitude is larger than that of the 31P−1H couplings, which ranged from 0.5 to 1.6 Hz.

Excess Proton Hydrate Structures with Large Proton Polarizability, Screened by Tris(2-ethylhexyl) Phosphate

Complexes of tris(2-ethylhexyl) phosphate (EHPO) with HAuCl4 and its hydrates with various amounts of water were studied by FT-IR spectroscopy. In the water free solution of HAuCl4 in EHPO homoconjugated PO···H+···OP hydrogen bonds with proton polarizability are formed. We demonstrate that in the 1:1 and 1:2 mixture with water only the H5O2+ species is present and no H3O+ species is formed. In the 1:1 mixture with water in addition to the H5O2+ species, 50% homoconjugated hydrogen bonds of protonated EHPO are still present. This homoconjugated hydrogen bond, as well as the central bond in H5O2+ shows large proton polarizability, as indicated by IR continua. In the 1:3 mixture of the homoconjugated complex with water a cyclic hydrogen-bonded system with a three-minima proton potential is present. The proton polarizability of this system is the largest, as indicated by a particularly intense IR continuum. In the case of the 1:4 mixture, a cyclic hydrogen-bonded arrangement with a four-minima proton potential is present, in which the barriers between the minima are larger than in the three-minima potential.

Constructing a short C–H · · · O hydrogen bond: the crystalline complex of triphenylsilylacetylene with triphenylphosphineoxide. A very unusual crystal structure with Z = 7 and Z′ = 3.5

The crystalline complex of triphenylsilylacetylene (Ph3Si–CC–H) and triphenylphosphineoxide (Ph3PO) contains four symmetry independent molecular dimers which are connected by CC–H · · · OP hydrogen bonds. These hydrogen bond have H · · · O separations between 1.99 and 2.05 A, and are the shortest reported for acetylenic donors. This reflects the fact that the hydrogen bonds are formed between one of the strongest known C–H donors and one of the strongest O acceptors. The red-shift of the acetylenic IR C–H stretching vibration compared to an apolar solution is -149 cm-1, the largest reported for a known crystal structure. The crystal packing in space group P is complex with the very rare unit cell content of 3.5 formula units per asymmetric crystal unit (Z′ = 3.5).

Proton polarizability of poly(L‐tyrosine)–hydrogen phosphate hydrogen bonds as a function of alkali cations

AbstractWe studied films of poly(L‐tyrosine) with hydrogen phosphate (residue/phosphate, 1:1) by ir spectroscopy. The influences of the alkali cations (Li+, Na+, K+) and of the degree of hydration were clarified. If Li+ ions are present, the OH ⃛−OP hydrogen bonds formed in the dried films between the tyrosine OH groups and hydrogen phosphate are asymmetrical. The formation of hydrogen phosphate–hydrogen phosphate hydrogen bonds is prevented by the presence of the Li+ ions. With an increase in the degree of hydration, the tyrosine–phosphate bonds are not broken but become slightly stronger. Completely different behaviour is found if K+ ions are present. In dry films, the OH ⃛−OP ⇌ O− ⃛HOP hydrogen bonds formed between tyrosine and hydrogen phosphate show large proton polarizability. The tyrosine proton has a noticeable residence time at the acceptor O atom of the phosphate. The difference in the behaviour of the system with K+ ions when compared to the system with Li+ ions can be explained, since the hydrogen acceptor O atom of phosphate ions is more negatively charged due to the weaker influence of the K+ ions. Furthermore, POH ⃛−OP hydrogen bonds between hydrogen phosphate molecules are formed. With an increase in the degree of hydration, the tyrosine–hydrogen phosphate hydrogen bonds are broken, all tyrosine protons are found at the tyrosine residues, and the ‐PO3− groupings are in a symmetrical environment, indicating that the K+ ions are removed from these groupings. If the degree of hydration increases further, hydrogen‐bonded systems such as hydrogen phosphate–water–hydrogen phosphate are formed that show large proton polarizability due to collective proton motion. When Na+ ions are present, the OH ⃛−OP ⇌ O− ⃛HOP hydrogen bonds formed in dry films still show proton polarizability, but the residence time of the tyrosine proton at the phosphate is very short.

Strong hydrogen bonding between imidazole and trimethyl phosphate

A new crystalline 1:1 complex of imidazole and trimethyl phosphate has been prepared and its i.r. and n.m.r. spectra reveal the presence of strong asymmetrical N–H ⋯ OP hydrogen bonds.

Polarisable Hydrogen Bond Formation and Ionic Interactions in Model Phospholipid Polar Head Molecules

The serine phosphoric acid P-methylester (SPM) and the ethanol-amine phosphoric acid P-methylester (EPM) were synthesized as water soluble models for the functional groups of the corresponding phospholipids. Investigations were made of the aqueous solutions of these molecules as a function of deprotonation and protonation. An intramolecular, easily polarisable hydrogen bond occurs in the zwitterion of the SPM. The solutions of different salts of SPM were studied as well as the influence of counter ion pairs. Counterion pairs hardly influence these bonds. At about 50% deprotonation extremely easily polarisable intermolecular bonds form. At about 100% deprotonation of the zwitterion the hydrogen bonds observed are affected by the presence of CO2. The above is indicated by changes of the bands of the carboxylic and phosphate groups, and in particular by a continuous absorption in the infrared spectrum. During protonation of the EPM easily polarisable intermolecular POH+ ... OP hydrogen bonds form at first, but as protonation increases the solutions become acidic, that is, H5O2 + groupings form.