Medium-strong Hydrogen Bonds Research Articles

Cooperative interaction of H3O+ with 1,3‐alternate tetrapropoxycalix[4]arene: NMR and theoretical study

Interaction of H3O+ or H5O2+ with 1,3-alternate tetrapropoxycalix[4]arene (1) was studied in nitrobenzene and dichloromethane using 1H and 13C NMR including transverse and rotating-frame relaxations and density functional level of theory (DFT) quantum calculations. According to NMR, the ion forms an equimolecular complex with 1 with the equilibrium constant K being 3.97 x 10(3) L.mol(-1) at 296 K. The ions are bound by strong hydrogen bonds to the phenoxy-oxygen atoms of one half of 1 and by a medium-strong hydrogen bond to the pi system of the aromatic rings of the other half. The complex appears to have C(4h) symmetry in NMR even when cooling its solution down to 213 K, which could be due either to a genuine symmetry of the complex (if the ion is H5O2+) or to fast structure averaging by ion exchange processes (if the ion is H3O+). Therefore, the dynamics of the system was studied. Using two independent NMR methods (transverse and rotating-frame relaxation), two different exchange processes were discerned with correlation times 25 x 10(-6) and 5 x 10(-6) s, the first being clearly intermolecular and the other being apparently intramolecular. The energetic aspects of the possible exchange processes were examined by DFT quantum calculations. Rotation of H3O+ ion within one binding site with the energy barrier 8.13 kcal/mol is easily possible. Intermolecular exchange by freeing the ion from the complex has too high a barrier but cooperative interaction of the ion with additional water molecules makes it viable. The intramolecular exchange (or hopping) of the H3O+ ion between the two sites of the molecule is not viable in the classical manner, the barrier being 25.6 kcal/mol. Quantum tunneling of the ion is highly improbable, too. Alternative mechanisms including concerted two-ion intermolecular exchange and cooperative interaction with another bound water molecule including complexation with proton dihydrate H5O2+ are discussed.

Vibrational spectra, X‐ray and molecular structure of 1H‐ and 3H‐imidazo[4,5‐b]pyridine and their methyl derivatives: DFT quantum chemical calculations

AbstractMolecular structure, vibrational energy levels and potential energy distribution of 1H‐imidazo[4,5‐b]pyridine, 3H‐imidazo[4,5‐b]pyridine, 5‐methyl‐1H‐imidazo[4,5‐b]pyridine, 6‐methyl‐1H‐imidazo[4,5‐b]pyridine and 7‐methyl‐3H‐imidazo[4,5‐b]pyridine were determined using density functional theory (DFT) at the B3LYP/6‐31G(d,p) level. The optimised bond lengths and bond angles are in good agreement with the X‐ray data of 5‐methyl‐1H‐imidazo[4,5‐b]pyridine obtained in the present work (Pbca space group; a = 8.660(2), b = 11.078(2), c = 11.078(3) Å, Z = 8). The N+H group plays the role of a proton donor in a medium strong hydrogen bond of the type NH…N, linking the N‐atom of the pyridine with the adjacent molecule related by the symmetry operation: 1/2 − x, y − 1/2, z(N…N = 2.869(25) Å). The presence of hydrogen bond is confirmed by appearance in the IR spectra of a very broad and strong contour in the 2000–3100 cm−1 range. The place of substitution of the methyl group at the pyridine ring influences the proton position of the NH group at the imidazole unit. Copyright © 2007 John Wiley & Sons, Ltd.

X-ray and ab initio studies of the structure, vibrational and NMR spectra of 1-methyl-3-hydroxypyridinium chloride

The crystal and molecular structure of 1-methyl-3-hydroxypyridinium chloride, MePY3OHCl, has been characterized by X-ray diffraction, FTIR and NMR spectra and ab initio calculations. The crystals are orthorhombic, space group Pnma, with four formula units in a cell of the dimensions a = 15.1698(11), b = 6.8029(7), c = 7.0298(6) Å. The Cl − anion is engaged in a medium-strong hydrogen bond with the O–H group (O⋯Cl − = 2.985(2) Å) and in three N +⋯Cl − intermolecular electrostatic interactions. The calculated O⋯Cl − distances are shorter than in the crystal. The experimental solid-state vibrational spectra of MePY3OHCl and MePY3ODCl have been tentatively assigned on the basis of B3LYP/6-31G(d,p) calculated frequencies and intensities. Correlations between the experimental 1H and 13C NMR chemical shifts for MePY3OHCl and GIAO calculated magnetic isotropic shielding tensors ( σ), δ exp = a + bσ cal, are reported.

A long Nb=O double bond in bis(pyridinium) tetrachlorooxo(pyridine-κN)niobate(V) chloride

The asymmetric unit of the title compound, (C 5 H 6 N) 2 -[NbCl 4 O(C 5 H 5 N)]Cl or (pyH)2[O=NbCl 4 (py)]Cl (py is pyridine), contains a discrete anionic niobium(V) complex, [O=NbCl 4 (Py)] - , and two protonated pyridine molecules, which form medium-strong hydrogen bonds with the Cl - counter-ion. The Nb=O distance of 1.7643 (17) A is the longest among those in congener niobium complexes reported to date. Extensive density functional theory studies of conformations of [O=NbCl 4 (py)] - and structural data mining raise doubts regarding the reliability of the length of this Nb=O double bond.

Structure, conformation and hydrogen bonding of 4-( N-methylpiperidinium)-butyric acid bromide

A 1:1 complex between 4-( N-methylpiperidinium)-butyrate inner salt (betaine) and hydrobromide, MPBUH·Br, has been characterized by single crystal X-ray analysis. The crystals are monoclinic, space group P2 1/c, with a = 8.284(1), b = 10.369(1), c = 13.809(2) Å, β = 92.26(1)°. The piperidine ring adopts a chair conformation with the (CH 2) 3COOH substituent in the axial and the CH 3 group in the equatorial positions. In the crystal, the Br − anion is engaged in a medium-strong hydrogen bond with the COOH group (O H⋯Br − = 3.141(1) Å), N +⋯Br − electrostatic interactions and in several C H⋯Br − contacts with the aliphatic groups forming a cavity in which it is enclosed. Three conformers ( 2– 4) were optimized by the B3LYP/6-31G (d, p) level of theory. The most stable is conformer 4 with the (CH 2) 3COOH substituent in the equatorial position and the CH 3 group in the axial position. The stability of the investigated conformers is controlled by electrostatic interactions between the oppositely charged groups. The FTIR spectrum of MPBUH·Br shows a strong band at 2941 cm −1 due to νOH and the νC O band at 1712 cm −1.

Hydrogen bonds and conformational analysis of bis(1-methylisonicotinate) hydrochloride monohydrate by X-ray diffraction, vibrational spectra and B3LYP calculations

In the crystal structure of bis(1-methylisonicotinate) hydrochloride monohydrate, (MIN) 2H·Cl·H 2O, 1-methylisonicotinate betaines are hemiprotonated and form a homoconjugated cation through a short asymmetric O·H·O hydrogen bond of length 2.456(3) Å. Water molecules and Cl − anions are linked alternatively by hydrogen bonds of lengths 3.202(3) and 3.282(2) Å into planar zigzag chains along the [ c] direction. The Cl − anion additionally interacts electrostatically with two positively charged nitrogen atoms of the neighboring MIN molecules. The most stable conformers of (MIN) 2H·Cl·H 2O, (MIN) 2H·Cl, (MIN) 2H·H 2O and (MIN) 2H have been analyzed by the B3LYP/6-31G(d,p) calculations in order to determine the influence of the anion and water molecule on the hydrogen bond in the homoconjugated MIN·H·MIN unit. The FTIR spectrum of (MIN) 2H·Cl·H 2O shows a broad and intense absorption in the 1500–400 cm −1 region, typical for short hydrogen bonds. The bands at 3416 and 3378 cm −1 confirm the presence of medium–strong hydrogen bonds between water molecules and Cl − anions.

Conformational analysis of bis(trigonelline) hydrochloride, perchlorate and their monohydrates by the B3LYP calculations, X-ray diffraction and vibrational spectra

In the crystal structure of bis(trigonelline) hydrochloride monohydrate, (TRG) 2H·Cl·H 2O, the trigonelline units are hemiprotonated and form homoconjugated cations through short asymmetric O·H·O hydrogen bonds of 2.456(4) Å in length. The H-bonded proton is closer to TRG which has shorter contacts with Cl − anion. The water molecules and Cl − anions are linked alternatively by hydrogen bonds of lengths 3.247(5) and 3.354(4) Å into planar zigzag chains along the [ z] direction. The Cl − anion additionally displays electrostatic interactions with two positively charged nitrogen atoms of the neighboring TRG molecules. The two most stable conformers of (TRG) 2H·Cl·H 2O, three of (TRG) 2H·ClO 4·H 2O and eight others were analyzed by the B3LYP/6-31G(d,p) calculations in order to determine the influence of the anions and water molecule on the hydrogen bond in the homoconjugated TRG·H·TRG unit. The FTIR spectrum of (TRG) 2H·Cl·H 2O shows a broad and intense absorption in the 1500–400 cm −1 region, typical of short hydrogen bonds. The band at 3383 cm −1 confirms a medium–strong hydrogen bonds between the water molecules and Cl − anions. In the complex crystallized from CH 3OD this broad absorption is replaced by two bands at 2500 and 1900 cm −1, which are similar to those in the spectra of TRG·D 2O and TRGD·Cl, respectively.

CsGa(H1.5AsO4)2(H2AsO4) and isotypic CsCr(H1.5AsO4)2(H2AsO4): decorated kröhnkite-like chains in two unusual hydrogen arsenates

Hydrothermally synthesized caesium gallium(III) hydrogen arsenate(V), CsGa(H1.5AsO4)2(H2AsO4), (I), and isotypic caesium chromium(III) hydrogen arsenate(V), CsCr(H1.5AsO4)2(H2AsO4), (II), represent a new structure type and stoichiometry among MI-MIII hydrogen arsenates. The crystal structure, determined from single-crystal X-ray diffraction data, is based on an infinite octahedral-tetrahedral chain and can be described as a decorated kröhnkite-like chain. The chains extend parallel to [100] and are separated by ten-coordinated Cs atoms. The hydrogen-bonding scheme comprises one very short symmetry-restricted hydrogen bond, with O...O distances of 2.519 (4) and 2.508 (4) A in (I) and (II), respectively, and two further medium-strong hydrogen bonds, all of which reinforce the connections between adjacent chains. The average Ga-O and Cr-O bond lengths are 1.973 (15) and 1.980 (13) A, respectively, and the average As-O bond lengths in the two protonated arsenate groups lie within a very narrow range [1.690 (18)-1.69 (3) A]. The Cs atom is located on a centre of inversion, while the MIII and As2 atoms lie on twofold axes. Relationships to CaBa2(HPO4)2(H2PO4)2 and other compounds containing decorated kröhnkite-type or kröhnkite-like chains are discussed.

Cs2CoII(C2O4)2·4H2O

Dicaesium cobalt(II) dioxalate tetrahydrate [tetraaquabis(μ-oxalato)cobalt(II)dicaesium(I)], Cs2CoII(C2O4)2·4H2O, has a layered structure and is isotypic with Cs2Mg(C2O4)2·4H2O. The unique Co atom shows octahedral coordination, with a mean Co—O bond length of 2.084 A. The Cs atom is irregularly coordinated by nine O atoms. Layers of CoO4(H2O)2 octahedra, whose non-water O ligands belong to nearly planar bidentate oxalate groups, are separated by corrugated layers of Cs atoms. Medium-strong hydrogen bonds provide connections within the layer planes. All atoms are in general positions except the Co atom, which lies on a twofold axis.

Crystal and molecular structure of N-methylpiperidine betaine hydrochloride

A 1:1 complex between N-methylpiperidine betaine and hydrochloric acid, MPBH·Cl, has been characterized by single crystal X-ray analysis, FTIR spectroscopy, and DFT calculations. The crystals are monoclinic, space group P2 1/ n, with a=6.0644(3), b=13.0220(6), c=12.7653(7) A ̊ , β=101.925(5)°. The piperidine ring adopts a chair conformation with the –CH 2COOH group in an axial and the-CH 3 group in an equatorial position. In the crystal, the Cl −anion is engaged in a medium-strong hydrogen bond with the COOH group (O–H⋯Cl −=2.9503(7) Å), in several C–H⋯Cl − contacts and, additionally, in three N +⋯Cl −intermolecular interactions. Four conformations (axial and equatorial, both protonated and unprotonated) of MPBHCl were examined by the B3LYP/6-31G(d,p) method. The calculated structure of MPBH·Cl(ax) is very similar to that in the crystal, except the N(1)–C(8)–C(9)–O(1) and N(1)–C(8)–C(9)–O(2) units, which are planar in the crystal but nonplanar in the isolated molecule. Powder FTIR spectra of MPBH·Cl and its deuterated analogue (MPBD·Cl) were measured and assignments of the observed bands to vibrations of the hydrogen bond and to internal vibrations are proposed.

Transformation of ammonium dicyanamide into dicyandiamide in the solid.

Ammonium dicyanamide NH(4)[N(CN)(2)] was synthesized through aqueous ion exchange. The crystal structure was investigated by single-crystal X-ray diffraction (P2(1)/c, a = 378.67(6) pm, b = 1240.9(3) pm, c = 911.84(14) pm, beta = 91.488(18) degrees, Z = 4). It derives from the CsCl structure type. Medium strong hydrogen bonds between NH(4)(+) and [N(CN)(2)](-) ions are indicative of the observed formation of dicyandiamide H(4)C(2)N(4) during heating. According to DSC and temperature-dependent X-ray powder diffractometry, this isomerization is exothermic and occurs between 102 and 106 degrees C in the solid. The reaction represents the isolobal analogue to the classical synthesis of urea by heating NH(4)OCN. While other alkali and alkaline earth dicyanamides undergo trimerization or polymerization of their anions during heating, ammonium dicyanamide thus shows a different reactivity.

Femtosecond Mid-Infrared Pump–Probe Study of Wave Packet Motion in a Medium-Strong Intramolecular Hydrogen Bond

Abstract We inspect the O–H stretching vibration of the medium-strong hydrogen bond in phthalic acid monomethyl ester in nonpolar solution by use of single-colour spectrally integrated femtosecond mid-infrared spectroscopy. We derive amplitude and phase characteristics of the coherent modulations of the pump-probe signals as a function of excitation wavelength. We exclude the role of Fermi resonances in the oscillatory contribution to the pump–probe signals. The observed periodic feature is due to wave packet motion of an underdamped out-of-plane 100 cm-1 mode that modulates the hydrogen bond distance. This low-frequency mode anharmonically coupled to the O–H stretching vibration is impulsively excited by the ultrashort mid-infrared pump pulse.

Observation of attractive intermolecular C–H⋯O interaction in the crystal packing of 3-chloro- and 3-bromo-2,6-dimethyl-4-nitropyridine N-oxide

Abstract The X-ray crystal structure determination of 3-chloro-2,6-dimethyl-4-nitropyridine N-oxide (ClDMNPNO) and 3-bromo-2,6-dimethyl-4-nitropyridine N-oxide (BrDMNPNO) shows that the two pyridine derivatives are isomorphic with monoclinic space group P21/c, and four formula units in a cell with the following dimensions: a=7.933(1), b=9.721(1), c=11.419(1) A, β=107.70(1)° and a=7.981(1), b=9.817(2), c=11.515(1) A, β=106.54(1)° for ClDMNPNO and BrDMNPNO, respectively. The shortest intermolecular contacts form medium strong hydrogen bonds of the type C–H⋯O. Another relatively short intermolecular contact is established for CH3⋯Cl/Br. The planar pyridine rings do not show the C–C bonds alternation typical for resonance forms in aromatic rings. The IR and Raman spectra, measured in the 50–3500 cm−1 region at ambient temperature, are correlated with X-ray structural data. The assignment of IR and Raman bands is given. Comparison of the spectra of dissolved samples with the ones obtained from polycrystalline samples shows the attractive character of the intermolecular C–H⋯O contact for these molecules. No strong spectroscopic support is found for the existence of a significant CH3⋯Cl/Br intermolecular interaction.

The unique molecular disorder of crystalline 4-chloro-2,6-dimethyl-3-iodopyridine N-oxide. An X-ray and spectroscopic study

The crystal structure of 4-chloro-2,6-dimethyl-3-iodopyridine N-oxide has been determined at ambient temperature. The compound crystallizes in monoclinic structure, space group P21/n. The asymmetric unit consists of two formula units, one of which shows positional disorder. The shortest intermolecular contacts form a medium strong hydrogen bond of the type C–H · · · O. The IR and Raman spectra, measured in the region 50–3500 cm–1, are in agreement with predictions based on the X-ray structural data. The observed electron absorption bands have been attributed to transitions between singlet levels, whereas the emission originates from transitions between the excited triplet level and the ground singlet level. The splitting of the strongest absorption band (225–242 nm) into three components has been explained to be a result of expansion of the valence shell of the iodine atom (d-orbital resonance).

Cooperative and isotope effects in complexes involving hydrogen chloride in solid argon

Abstract The cooperativities for B⋯(HCl) 2 and B⋯(DCl) 2 complexes in solid argon are discussed. The cooperativities are much higher for the van der Waals complexes than for the medium-strong hydrogen bonds. The zero-point energy differences between the H- and D-bonds are calculated by the theory of Buckingham and Lin (A.D. Buckingham and F.C. Lin, Int. Rev. Phys. Chem., 1 (1981) 253). The results show that with the exception of the complexes involving the strong bases pyridine and pyridine N -oxide, the D-bonds are slightly stronger than their H counterparts. The difference between the D/H energies shows a tendency to decrease with increasing strength of the interaction. These conclusions agree qualitatively with data obtained from rotational spectroscopy (A.C. Legon and D.J. Millen, Chem. Phys. Lett., 147 (1988) 484).

A new semiempirical potential function for hydrogen bonds and its possible use in studying the DNA molecule

Abstract A semiempirical potential function V ( r,R ) is proposed for describing the protons in hydrogen bonds. It consists of: the Morse potential V A ( r ), which describes the covalent bond AH in the R 1 AH⋯BR 2 system; a Coulombic term E e.s. , which contains the Coulombic point interaction of each atom of the R 1 AH group with the BR 2 molecule and the interaction of the hydrogen atom with the R 1 A group having non-equilibrium lengths R  R 0 ; the potential V R ( R ), which describes the exponential repulsion of atoms A and B owing to the partial overlap of their shells; another Morse potential V B ( R—r ), which accounts for all other effects such as the redistribution of charge density by the approach of the hydrogen and boron atoms, their mutual polarization, and partly also Van der Waals forces. The parameters of the proton potential were found for the (H 2 O) 2 dimer and for three hydrogen bonds of a guanine—cytosine (GC) pair for weak and medium strong hydrogen bonds without high proton excitation levels. Using the dependence on R of the bond energy ϵ( R ) (for the water dimer) and the V ( r,R ) values at R = R 0 (for the GC pair), we extrapolated the V ( r,R ) functions to non-equilibrium r = R 0 and R = R 0 values. A simple method of solving a one-dimensional Schrodinger equation is proposed for such a potential function. Wavefunctions and the corresponding energy levels were obtained. These data make it possible to study the influence of hydrogen bonds in the ground and excited states on the character of the atomic vibrations in the GC pair and the processes in poly-GC with one adenine-thymine pair by absorption of excess energy and also the influence of dielectric surroundings (in particular, water) on the properties of the hydrogen bonds in (H 2 O) 2 .

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.

Scandium, yttrium and lanthanum phosphites

The M 2( HPO 3) 3 · nH 2 O, MH 3 P 2 O 6· nH 2 O and MH 6 P 3 O 9· nH 2 O phosphites (M ≡ Sc, Y, La; n = 1.5–18 were isolated at 25 °C in ternary M 2(HPO 3) 3-H 3PO 3-H 2O systems (M ≡ Sc, Y, La) on the basis of a solubility study. The compounds prepared were studied by thermography, X-ray analysis and IR molecular spectroscopy. In M 2( HPO 3) 3 · nH 2 O compounds (M ≡ Y, La) a deformed HPO 3 2− anion (of symmetry C s ) is present; this is positively hydrated by water molecules. Hydrogen phosphites contain complicated anions with medium-strong hydrogen bonds of the P-O-H … O-P type.

Hydrogen bond studies. CXXXVIII. Neutron diffraction studies of LiNO3.3H2O at 120 and 295 K

For pt.CXXXVII see ibid., vol.B35, p.2384 (1979). LiNO 3.3H 2O has been studied by neutron diffraction at 120 and 295 K. The final R(w.F 2) values are 4.5% (120K) and 4.9% (295K). The crystal structure found in a previous room-temperature X-ray study is confirmed: one water molecule is involved in six hydrogen bonds; the other independent water molecule in the structure has a tetrahedral environment comprising two Li + ions and two medium-strong hydrogen bonds. The four different O...O hydrogen-bond lengths increase by 0.02-0.03 Aring going from 120 to 295K. The mean-square amplitudes of vibration for the N and O atoms are found to be closely proportional to temperature. For the H and Li atoms the vibrational amplitudes are less sensitive to temperature. Crystal data: space group Cmcm, Z=4; at 120K a=6.713 (7), b=12.669 (4), c=5.968 (5) Aring; at 295K a=6.8018 (4), b=12.7132 (9), c=5.9990 (4) Aring.