NHO Hydrogen Bond Research Articles

Conformational analysis of 5-piperidinevaleric acid, 5-(N-methylpiperidine)valerate and their hydrogen halides by MO calculations, X-ray diffraction and FTIR spectroscopy

The most stable conformers of 5-(piperidine)valeric acid (1), 5-(N-methylpiperidine)valerate (2) and their hydrogen halides (3 and 4) were analyzed by the semiempirical PM3 method and selected compounds by the B3LYP/6-31G(d,p) method. As some of the investigated compounds are charged and the others can be neutral, some have acidic proton, others do not. They are capable of forming ionic bonds (via Coulombic attraction between the oppositely charged groups) or of forming the various types of hydrogen bonded conformers. As a result these compounds are ideally suited to study the importance of electrostatic interactions and hydrogen bonding on the relative stabilities of conformers. In the case of compounds containing N-methylpiperidine unit, for a particular conformer, the intramolecular attractive electrostatic interactions between the charged group play key roles in their relative stability in the gas phase. The electrostatic interaction of the X− ion with the positively charged nitrogen atom decreases their proton-acceptor properties and COOH⋯X− hydrogen bonds are present in all hydrogen halides (3). 5-Piperidine valeric acid with HF forms a molecular complex, while with HCl, HBr and HI an ion pair, according to the B3LYP calculations. The PM3 calculations predict a molecular complex also with HCl. The crystal structure of 5-(piperidine)valeric acid hydrogen bromide (4HBr), space group of crystals P21/n with a=6.204(1), b=32.777(7), c=6.416(1)Å, β=106.21(3)°, Z=4 and R=0.0685 was characterised by X-ray crystallography methods. Br− ion forms two types of hydrogen bonds: Br⋯N(1), 3.247(14)Å, and O(1) ⋯Br, 3.118(11)Å. Moreover, C–H⋯Br short contacts, which can be recognized as weak hydrogen bonds, exist in the crystal. The FTIR spectrum of 1 in the solid state shows an intense broad absorption in the 1600–400cm−1 region typical for a very short NHO hydrogen bonds. In solution the hydrogen bond seems to be longer. The bands of νCO at 1708cm−1 and νasCOO− at 1615cm−1 in CD3CN solution show that OH⋯N⇌O−⋯HN+ equilibrium exists. Ab initio calculations predict molecular structures of three most stable conformers of 1 in the gas phase.

Conformations of, and NHO hydrogen bond in, piperidine-1-valeric acid and its dihydrate

Effects of hydration on hydrogen bonding and conformation of the amino acid, piperidine-1-valeric acid (PIPVAL), have been studied by X-rays, FTIR and quantum chemical calculations. PIPVAL forms anhydrous and dihydrate crystals. In PIPVAL·2H2O two zwitterionic molecules are linked by a pair of identical N+–H· · ·O hydrogen bonds of 2.684(4) A into a cyclic centrosymmetric dimer. The dimers form a network of hydrogen bonds with water molecules. The conformation of anhydrous PIPVAL was studied by semiempirical and ab initio calculations. Two cyclic dimers were derived by the PM3 method (neutral and zwitterionic, with the former being 50 kcal mol–1 more stable) and only the neutral one at the SAM1 and HF levels. The solid state FTIR spectra of the anhydrous and dihydrate crystals are considerably different. The spectrum of PIPVAL·2H2O reflects the N+–H· · ·O hydrogen bond determined by X-rays. The broad and intense absorption in the 1600–400 cm–1 region resulting from the much shorter hydrogen bond N+–H· · ·O of about 2.5 A is observed in the anhydrous acid. This comparison clearly illustrates the specific features of amino acids associating with water, present in all living organisms.

Structure of (C 3H 5NH 3) 2H 2P 2O 7·H 2O

The bis(cyclopropylammonium)dihydrogenodiphosphate monohydrate is a new diphosphate associated with the organic molecule C 3H 5NH 2. We report the chemical preparation and the crystal structure of this organic cation diphosphate. (C 3H 5NH 3) 2H 2P 2O 7.H 2O is orthorhombic (S.G. : P2 12 12 1), with Z = 4 and the following unit-cell parameters : a = 4.828(1) Å, b = 11.011(1) Å, c = 25.645(2) Å. The P 2O 7 groups and H 2O water molecules form a succession of bidimensional layers perpendicular to the c axis. The organic cations ensure the three-dimensional cohesion by NH-O hydrogen bonds.

Effects of specific interactions on the anisotropy of crystal structure distortion of [Co(NH3)5NO2]Cl2 under hydrostatic pressure

Using some special experimental techniques for anisotropic refinement of the crystal structure of [Co(NH3)5NO2]Cl2 at high pressures gave results with an accuracy comparable to that obtained in normal conditions. The anisotropy of lattice compression under pressure is determined by specific interactions in crystals, in particular, by NH-Cl and NH-O hydrogen bonds. The anisotropy of compression at increased pressure is qualitatively distinct from that caused by lowered temperature for the same structure. This difference is also due to specific interactions (hydrogen bonds) in the structure.

Proton Dynamics in Interacting Hydrogen Bonds in the Solid State: Proton Tunneling in the NHO Hydrogen Bonds of N,N′‐Di(2‐Hydroxy‐1‐Naphthylmethylene)‐p‐Phenylenediamine

AbstractCombination of comprehensive investigations of the spin‐lattice relaxation rate of proton and low temperature 15N‐CP/MAS NMR spectrum provides unique information of proton dynamics in two interacting NHO hydrogen bonds of solid N,N′‐di(2‐hydroxy‐1‐naphthylmethylene)‐p‐phenylenediamine (DNP). It was evidenced from the 1H‐NMR relaxation measurement that tunneling mechanism operates for the proton transfer in the hydrogen bonds. The tunneling phenomenon is closely related to the very small energy differences among the four tautomeric states accompanied with the proton transfer in the two NHO hydrogen bonds. The very small values of the energy difference, in spite of the chemically asymmetric NHO hydrogen bond, were revealed by the 15N‐CP/MAS NMR spectrum. This is a unique character of solid DNP. It was also suggested from the derived energy scheme of the four tautomers and activation energies of the proton transfer that an interaction exists between the two NHO hydrogen bonds linked by π‐electronic molecular frame. This means that the information of one NHO hydrogen bond, i.e. OH‐form or NH‐form, propagates to the other hydrogen bond and the proton transfer in the first hydrogen bond induces the change of the potential function for the proton transfer in the second hydrogen bond.

Observation of thermal tautomerism of thermochromic salicylideneaniline derivatives in the solid state by 15N CPMAS NMR down to cryogenic temperatures

AbstractThe temperature dependent solid state 15N CPMAS NMR spectra of 15N enriched salicylideneaniline derivatives, N‐salicylideneaniline (SA), N,Nî‐bissalicylidene‐p‐phenylenediamine (BSP) and N,Nî‐di(2‐hydroxy‐1‐naphthylidene)‐p‐phenylenediamine (DNP) were measured in order to study possible proton transfer processes in the NHO hydrogen bonds. For DNP a remarkable change of the 15N chemical shifts of more than 50 ppm was observed between 26 and 388 K by using the CPMAS NMR technique down to cryogenic temperatures. The result clearly indicates very small enthalpy differences among the four tautormers associated with the combination of two possible forms, OH and NH form, of the two NHO hydrogen bonds in a DNP molecule.

Crystal structure of 1-hydroxy-1,2,3-benzotriazolium diphenyl phosphate reveals strong NHO and OHO hydrogen bonds

The structure of 1-hydroxy-1,2,3-benzotriazolium diphenyl phosphate (HOBt/DPP) has been investigated by X-ray analysis. The compound crystallizes in the monoclinic space group P2 1 n with Z = 4 and the following lattice parameters: a = 11.711(2), b = 12.727(2) and c = 12.794(3) A ̊ , β = 105.12(2)°, V = 1840.9(6) A ̊ 3 . The structure was solved by direct methods and refined on F 2 to R values of w R2 = 0.084 and R1 = 0.034 for 1985 observed reflections. HOBt/DPP has an ionic structure with very short OHO and NHO hydrogen bonds linking the different ions. Owing to these hydrogen bonds, infinite screw-shaped chains which are twisted parallel to the y-axis are formed.

水素結合における構造物性と機能 水素の運動

Developments of studies of hydrogen transfer dynamics and tunneling effect in a variety of hydrogen bonds in solids are reviewed. Particular attention was paid for interactions between the hydrogen transfer motion and the surrounding of the hydrogen bond. Those are phonon-assisted tunneling, information propagation between the two interacting NHO hydrogen bonds linked by π-electronic molecular frame, and a novel correlation effect on proton transfer in the proton/deuteron mixed system.

ESR study on the charge transfer complexes of N-salicylideneanilines containing NHO hydrogen bond as a dynamic function

Summary form only given. N-Salicylideneaniline derivatives have intramolecular NHO hydrogen bond. We have found that the barrier height for the proton transfer in the NHO hydrogen bond of these compounds is relatively small in the crystalline state and the proton transfer is accompanied by a configurational change of the /spl pi/-electron system, showing thermochromism in some cases. Thus in the charge transfer complexes of these N-salicylideneaniline derivatives (NN, NPY and DNP shown in the figure) with TCNQ and with F/sub 4/-TCNQ, a dynamic interaction between the hydrogen bond and the electronic state of the mixed stacking column of donor and acceptors may be expected. The ESR line shape of (NPY)/sub 2//F/sub 4/-TCNQ and NN/(TCNQ)/sub 2/ was simple lorentzian near 20 K and the line width decreased remarkably as temperature increased up to 300 K. This behavior is similar to that of t-polyacetylene and suggests a motion of the spin. A deuteration of the hydrogen bond of NN/(TCNQ)/sub 2/ led to a reduction of ESR line width. Delocalization of the proton in the hydrogen bond in the NPY and NN complexes was suggested by X-ray structure analysis. NMR measurements were also performed on the complexes.

NMR Study of Proton Dynamics in the Hydrogen Bonds in the Thermochromic Crystals ofN-salicylideneaniline derivatives

Abstract The crystals of several derivatives of N-salicylideneaniline which contain NHO hydrogen bonds in the molecule show thermochromism. To investigate the relation between the thermochromism and the proton transfer in the hydrogen bond, the proton dynamics of remarkably thermochromic crystal of BSP was precisely studied by solid state NMR method. The behavior of proton dynamics is good consistent with the temperature dependence of visible absorption spectra of this crystal. This result indicates that the thermochromism of this material is a prototype of “proton-electron cooperation”. The transfer rate of proton in the NHO hydrogen bond was strongly affected by some chemical modifications, e.g.the fast tunneling in one case.

NMR study of proton dynamics in the NHO hydrogen bonds in the thermochromic crystals of N-salicylideneanilines

The precise investigation of the spin—lattice relaxation rate of the proton of the remarkably thermochromic crystal of N,N′-bis(salicylidene)- p-phenylenediamine provides unique information of proton dynamics in the NHO hydrogen bonds, which is consistent with the temperature dependence of the visible absorption spectra of this crystal and which reveals the presence of interaction between two NHO hydrogen bonds in the molecule through rearrangement of the configuration of π-electrons. This result indicates that the thermochromism of this material is a prototype of “proton—electron cooperation”. The transfer rate of proton in the NHO hydrogen bond is strongly affected by a chemical modification, e.g. the fast tunneling.

A quantitative comparison of spectroscopic and energy data, in solution, of NHO and OHO hydrogen bonds and gas-phase proton affinities: complexes of pyridines and pyridine N-oxides with acetic acids

The correlations between the centre of gravity (ν H) of the broad IR vibrations, chemical shifts (δ H) of hydrogen-bonded protons and enthalpies of hydroben bonds (−Δ H) of two series of complexes (pyridines and pyridine N-oxides) with trifluoroacetic, dichloroacetic, chloroacetic and acetic acids, and the difference between the gas-phase proton affinity of bases ( PA(B)) and that of conjugate bases ( PA(A −)) were investigated. Complexes of pyridines with all these acids can be treated as one category and complexes of pyridine N-oxides as another. On the other hand, correlations of ν H and δ H with aqueous p K a values consist of separate lines for each acid. The PA(A −) and PA(B) values provide an excellent basicity scale for hydrogen bonds in solvents of low and medium polarity.

ChemInform Abstract: β‐Diketone Interactions. Part 11. The Hydrogen‐Bonded Adduct 4,6‐Dimethylpyrimidin‐2‐one·Urea (DMP·U) from the Reaction of Pentane‐2,4‐dione and Urea

The X-ray crystal Structure of the adduct formed between 4,6-dimethylpyrimidin-2-one and urea (DMP·U) shoes a compact unit joined through two N–H ⋯ OC hydrogen bonds. One of these is remarkably short with RN ⋯ O 2.735 A(RH ⋯ O 1.705 A), and is believed to be among the shortest example of an NHO hydrogen bond between neutral molecules. Its hydrogen-bond energy, estimated from IR data, is ca. 75 kJ mol–1

β-Diketone interactions. Part 11. The hydrogen-bonded adduct 4, 6-dimethylpyrimidin-2-one·urea (DMP·U) from the reaction of pentane-2,4-dione and urea

The X-ray crystal Structure of the adduct formed between 4,6-dimethylpyrimidin-2-one and urea (DMP·U) shoes a compact unit joined through two N–H ⋯ OC hydrogen bonds. One of these is remarkably short with RN ⋯ O 2.735 Å(RH ⋯ O 1.705 Å), and is believed to be among the shortest example of an NHO hydrogen bond between neutral molecules. Its hydrogen-bond energy, estimated from IR data, is ca. 75 kJ mol–1

Very strong NHO hydrogen bond in the complex of 3-oxo-azabicyclo[2.2.2]octane with pentachlorophenol

The structure of the complex of 3-oxo-azabicyclo[2.2.2]octane with pentachlorophenol (OAO PCP) has been determined by X-ray diffraction. The crystals are monoclinic, space group C2/ c, with a = 24.89(2), b = 9.667(6), c = 18.14(1) Å, β = 133.97(4)° and Z = 8. The structure solved by direct methods has been refined to R = 0.041 for 2810 non-zero reflections. The N⋯O distance of 2.514(5) Å is the shortest length of an NHO intermolecular hydrogen bond found so far. The protonic absorption continuum spreading in the 250–1500 cm −1 region is characteristic for the shortest hydrogen bonds in which the proton motion may be described by a potential energy curve with an unsymmetrical single minimum.

VERY STRONG HYDROGEN BONDING OF PHOSPHATES: X-RAY CRYSTAL STRUCTURES OF 1,2,3-BENZOTRIAZOLIUM DIHYDROGEN PHOSPHATE [C6H4N3H2 +][H2PO− 4] AND 1,3-BENZIMIDAZOLIUM DIHYDROGEN PHOSPHATE [C7H5N2H2 +][H2PO− 4

Abstract 1,2,3-Benzotriazole and 1,3-benzimidazole produce crystals of 1:1 adducts with H3PO4. Their X-ray structures reveal chains of phosphate ions linked through very short OHO hydrogen bonds. These chains are cross-linked through NHO hydrogen bonds to the 1,3-nitrogen atoms of the protonated bases. Although structurally similar, there are differences between the two systems–the ben-zotriazolium salt having shorter hydrogen bonds than the benzimidazolium salt. This is attributed not to their relvative basicities, but to crystal packing forces.

1,2,3-Benzotriazolium dihydrogen phosphate, [C6H4N3H2+][H2PO4–]: X-ray crystal structure reveals very strong hydrogen bonds

1,2,3-Benzotriazolium and H3PO4 produce crystals of a 1 : 1 adduct that has a structure composed of very short NHO and OHO hydrogen bonds linking the various ions and one oxygen atom in a unique chemical environment.

Raman and infrared spectra of spermidine and spermine and their hydrochlorides and phosphates as a basis for the study of the interactions between polyamines and nucleic acids

AbstractThe Raman and infrared spectra of the polyamines spermidine and spermine and of their corresponding hydrochlorides and phosphates have been studied. These systems can be regarded as models of the molecular interactions between polyamines and nucleic acids, and the observed spectra are discussed in relation to this. Medium strong and strong NHCl and NHO hydrogen bonds are present in both the polyamine hydrochlorides and phosphates and the proton is predominantly located on the nitrogen atom. In the case of the phosphates, the Raman spectra indicate the formation of HPO groups, which can also interact among themselves by strong OHO hydrogen bonds.

Refined crystal structure of carboxypeptidase a at 1·54 Å resolution

The crystal structure of bovine carboxypeptidase A (Cox) has been refined at 1.54 A resolution using the restrained least-squares algorithm of Hendrickson & Konnert (1981). The crystallographic R factor (formula; see text) for structure factors calculated from the final model is 0.190. Bond lengths and bond angles in the carboxypeptidase A model have root-mean-square deviations from ideal values of 0.025 A and 3.6 degrees, respectively. Four examples of a reverse turn like structure (the "Asx" turn) requiring an aspartic acid or asparagine residue are observed in this structure. The Asx turn has the same number of atoms as a reverse turn, but only one peptide bond, and the hydrogen bond that closes the turn is between the Asx side-chain CO group and a main-chain NH group. The distributions of CO-N and NH-O hydrogen bond angles in the alpha-helices and beta-sheet structures of carboxypeptidase A are centered about 156 degrees. A total of 192 water molecules per molecule of enzyme are included in the final model. Unlike the hydrogen bonding geometry observed in the secondary structure of the enzyme, the CO-O(wat) hydrogen bond angle is distributed about 131 degrees, indicating the role of the lone pair electrons of the carbonyl oxygen in the hydrogen bond interaction. Twenty four solvent molecules are observed buried within the protein. Several of these waters are organized into hydrogen-bonded chains containing up to five waters. The average temperature factor for atoms in carboxypeptidase A is 8 A2, and varies from 5 A2 in the center of the protein, to over 30 A2 at the surface.

PROPERTIES AND STRUCTURES OF NYLON 3 DERIVATIVES

Choosing α methyl nylon 3, β methyl nylon 3, α, α, dimethyl nylon 3, and β, β, dimethyl nylon 3 as the nylon derivatives, the effects of substituents on the properties and structures were investigated by the methods of X-ray diffraction, infra-red spectra, and thermal analysis, and following results were obtained. Melting points of the polymer increase with in following order. α, α, dimethyl<β, β, dimethyl<α methyl≤β mthyl_??_no substituent. The NH streching absorptions were observed at 3380cm-1 in α, α, dimethyl nylon 3, at 3340cm-1 in β, β, dimethyl nylon 3, and at 3300cm-1 in other nylons. NH--O distances of the derivatives are estimated, and melting point of the polymers and location of the NH streching absorptions were found to be mainly determined by the NH-O distances. Though nylon 3 derivatives belong to short methylene polyamides, a distort of molecular chain occurs around amide groups. This may be due to the favorable NH-O hydrogen bond distances under the steric hinddrances of the substituents.