Bent Hydrogen Bonds Research Articles

Quantum chemical investigation of stability and structure related to the geometrical isomerism of tautomeric forms of cytosine and uracil

The results of quantum-chemical calculations of the total electronic energies and fully optimized structural parameters of nine cytosine and nine uracil tautomers at the HF/3-21G-MP2/HF/6-31G ∗∗ level of approximation are reported. For five of the cytosine tautomers nonplanar equilibrium structures were found. The conversion energies of the geometrical isomers associated with OH substituents in the 2-position and NH or OH substituents in the 6-position of the pyrimidine ring system were derived from the total energies. A search for correlations between the geometrical isomers and internal structural parameters led to rules for the changes in the regional bond lengths and bond angles that occur upon interconversion of the isomers; these correlations in many cases can be expressed as linear regressions. The electronic conversion energies form a fairly complex pattern, but it proved possible to express these quantities additively by contributions which are intuitively perceptible from the structural formula, either as repulsive interactions between hydrogen atoms bound to ring atoms and hydrogen atoms of OH- or NH- (NH 2-) substituents or as attractive interactions between hydrogen atoms of the latter sort and electrons localized on the sp 2 lone-pair orbitais centered on the nitrogen atoms in the β-position. The attractive interactions may be classified as a hitherto unrecognized type of medium strength, strongly bent internal hydrogen bond. In order to arrive at a consistent set of energy-contribution terms, a set of 24 geometrical isomers of 10 model compounds (derivatives of propynoic acid) was investigated at the HF/6-31G ∗∗ level of theory. These model compounds served as reference systems for the determination of zeroth-order approximations to specific conversion-energy contributions. The quantum-chemical conversion energies of the geometrical isomers of cytosine and uracil, are reproduced within error limits from these contributions; this procedure seems to be fairly universally applicable.

Rotational spectrum of a short-lived dimer of oxirane and hydrogen chloride: Evidence for a bent hydrogen bond

Ground state rotational spectra of the three isotopomers (CH2)2O...H35Cl, (CH2)2O...H37Cl, and (CH2)2O...D35Cl of a short-lived hydrogen-bonded dimer have been detected in the reactive mixture of oxirane and hydrogen chloride by using a fast-mixing nozzle in conjunction with a Balle–Flygare Fourier-transform microwave spectrometer. Rotational constants, centrifugal distortion constants and Cl-nuclear quadrupole coupling constants were determined for each isotopomer. In particular, all four components χaa, χbb, χcc, and χac of the coupling tensor were obtained. A detailed analysis of the rotational constants allows the conclusion that the dimer has Cs symmetry, with a steeply pyramidal arrangement completed at oxygen by the hydrogen bond with HCl. Diagonalization of the complete Cl-nuclear quadrupole coupling tensor leads to the principal axis components χxx, χyy, and χzz (where z is the HCl direction in the dimer). The angle of rotation α is the angle between the HCl (z) direction and the a-axis direction in the equilibrium conformation of the dimer. It is larger by ∼10° than the angle γ between the O...Cl internuclear line and the principal inertial axis a in each case and implies that the hydrogen bond is bent by 180-θ=∼16.5° from the collinear arrangement O...H–Cl (θ=0). The angle 180-θ and the angle φ=76.2° made by the O...Cl internuclear line with the extension of the oxirane local C2 axis are interpreted in terms of a simple model of the hydrogen bond.

Energetics, proton transfer rates, and kinetic isotope effects in bent hydrogen bonds

N-N...N H-bonds which occur in intermolecular contacts and in intramolecular situations where the bond is bent are investigated by ab initio methods. Distortion of the O(N-H...N) angle of up to 40 o from linearity results in modest increases in the barrier to proton transfer while a much higher barrier occurs in NH 2 CH 2 NH 3 + where this angular distortion is some 100 o . The rate of transfer is orders of magnitude slower in the latter system. In contrast to earlier suppositions that systems containing nonlinear H-bonds are subject to smaller kinetic isotope effects, k H /k D for the most highly strained system is larger than in other complexes

Investigation of the rotational spectrum of the hydrogen-bonded dimer CF2CH2⋯HCl

Rotational spectra of three isotopic species of the hydrogen-bonded dimer formed between 1,1-difluoroethene and HCl have been obtained with pulsed-supersonic-nozzle Fourier-transform microwave spectroscopy. Analysis of the derived spectroscopic constants shows that the dimer is near planar with HCl bonded to fluorine via a ClH⋯F hydrogen bond and positioned cis to the vinyl group. There are also indications of a bent hydrogen bond and of participation of an interaction peripheral to the hydrogen bond in determining the geometry. Key structural features of the dimer are successfully predicted with the electrostatic model.

Rotational spectroscopy of a mixture of thiirane and hydrogen bromide: detection and characterization of a short-lived complex (CH2)2SċHBr in a pulsed jet

A hydrogen-bonded dimer formed by thiirane with hydrogen bromide has been detected and characterized in the gas phase by means of its ground-state rotational spectrum. The spectrum was detected within ca. 1 µs of the creation of the nascent dimer by using a fast mixing nozzle in conjunction with a pulsed-nozzle, FT microwave spectrometer. With the former device the reactive components thiirane and hydrogen bromide remain separate until they expand into the Fabry–Pérot cavity of the latter. Rotational constants A0, B0 and C0, centrifugal distortion constants ΔJ, ΔJK and δJ, Br nuclear quadrupole coupling constants χaa, χbb and χab, and Br spin–rotation coupling constants have been determined for each of the isotopomers (CH2)2SċH79Br and (CH2)2Sċ;H81Br. Interpretation of the various spectroscopic constants leads to the conclusion that the dimer has Cs symmetry, with HBr lying in the plane perpendicular to the thiirane heavy-atom plane and with a pyramidal arrangement at S. There is some evidence of a bent hydrogen bond. The angle ϕ≈ 80° made by the SċH line with the thiirane plane is discussed in terms of some simple rules for predicting angular geometries of hydrogen-bonded dimers and a non-bonding electron-pair model for thiirane.

Factors contributing to distortion energies in bent hydrogen bonds. 2. Imine, carbonyl, carboxyl, and carboxylate groups

The source of the energy requirement for bending a hydrogen bond is sought through decomposition of the total ab initio interaction energy into a number of physically meaningful components. Systems studied include (H 2 CNH-H-NH 3 ) + , (H 2 CO-H-OH 2 ) + , (HCOOH-H-OH 2 ) + , and (HCOO-H-OH) - . As in the earlier cases studied which had been restricted only to small hydride molecules, the Coulombic interaction very closely parallels the change in the total interaction energy as angular distortions are imposed. Despite the larger size of the current molecules and the arbitrariness in selecting an origin for expansion, a multipole series approximation truncated after the R -5 term mimics fairly well the full electrostatic component

Selective elimination of interactions: a method for assessing thermodynamic contributions to ligand binding with application to rhinovirus antivirals

A new method for evaluating the free energy of various physical interactions, such as hydrogen-bond, electrostatic, or van der Waals interactions, is presented. Rather than destroying or creating whole groups, selective (pairwise) interactions are eliminated from the total potential energy and the energy difference with the fully interacting system is evaluated. The exponential ensemble average of such an energy difference is then directly related to the corresponding free energy difference. This procedure is then applied to a rather large protein-ligand system involving the coat proteins of a human rhinovirus and an antiviral ligand. The results seem to indicate that a particular bent hydrogen bond between the ligand and protein system may not be favorable for binding. The method presented gives an estimate of the hydrogen bond free energy contribution with an available trajectory that was previously computed without the expenditure of sizeable computational resources such as recomputing a trajectory. This procedure is effective and efficient for computing the free energy for a given type of physical interaction. It can be used for calculating the binding energy differences for various interactions which can be used to guide the search for isosoluble synthetic targets.

Factors contributing to distortion energies of bent hydrogen bonds. Implications for proton-transfer potentials

ADVERTISEMENT RETURN TO ISSUEPREVArticleFactors contributing to distortion energies of bent hydrogen bonds. Implications for proton-transfer potentialsSlawomir M. Cybulski and Steve ScheinerCite this: J. Phys. Chem. 1989, 93, 17, 6565–6574Publication Date (Print):August 1, 1989Publication History Published online1 May 2002Published inissue 1 August 1989https://doi.org/10.1021/j100354a055RIGHTS & PERMISSIONSArticle Views40Altmetric-Citations30LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InReddit PDF (1 MB) Get e-Alerts

Water of crystallization and its hydrogen-bonded crosslinking in vivianite Fe3(PO4)2 · 8H2O; a neutron diffraction investigation

All the protons of the water of crystallization of vivianite Fe3(PO4)2 · 8H2O participate in bent hydrogen bonds of normal strength. Their geometry has been calculated from single crystal neutron diffraction data.

Relationship of normal modes and local modes to normal coordinate treatment of liquid water

A harmonically coupled degenerate anharmonic oscillator model has been developed to compute the intramolecular stretching frequency distribution H 2 O in liquid phase. Mathematical formulation of the problem is based on the Lippincott-Schroeder potential function for bent hydrogen bond systems and a formula can be obtained for the anharmonicity constant. Random molecules were generated by Monte Carlo method and the elgenvalues of the vibrational Hamiltonian versus oxygen-oxygen distances were computed. The true energy levels were obtained by introducing the effect of anharmonicity to the stretching normal frequencies.

Temperature dependence of the low- and high-frequency Raman scattering from liquid water

Low frequency Δν̄=0–350 cm−1, Raman intensity data were obtained from liquid water between 3.5 and 89.3 °C using holographic grating double and triple monochromators. The spectra were Bose–Einstein (BE) corrected, I/(1+n), and the total integrated (absolute) contour intensities were treated by an elaboration of the Young–Westerdahl (YW) thermodynamic method, assuming conservation of hydrogen-bonded (HB) and nonhydrogen-bonded (NHB=bent and/or stretched, O–H O) nearest-neighbor O–O pairs. A ΔH°1 value of 2.6±0.1 kcal/mol O–H ⋅⋅⋅ O or 5.2±0.2 kcal/mol H2O (11 kJ/mol O–H ⋅⋅⋅ O, or 22 kJ/mol H2O) resulted for the HB→NHB process. This intermolecular value agrees quantitatively with Raman and infrared ΔH° values from the one- and two-phonon OH-stretching regions, and from molecular dynamics, depolarized light scattering, neutron scattering, and ultrasonic absorption, thus indicating a common process. A population involving partial covalency of, i.e., charge transfer into, the H ⋅⋅⋅ O units of linear and/or weakly bent hydrogen bonds, O–H ⋅⋅⋅ O; is transformed into a second high energy population involving bent, e.g., 150° or less, and/or stretched, e.g., 3.2 Å, but otherwise strongly cohesive O–H O interactions. All difference spectra from the fundamental OH-stretching contours cross at the X(Z,X+Z)Y isobestic frequency of 3425 cm−1. Also, total integrated Raman intensity decreases occurring below 3425 cm−1 with temperature rise were found to be proportional to the total integrated intensity increases above 3425 cm−1, indicating conservation among the HB and NHB OH-stretching classes. From the enthalpy of vaporization of water at 0 °C, and the ΔH°1 of 2.6 kcal/mol O–H ⋅⋅⋅ O, the additional enthalpy, ΔH°2, needed for the complete separation of the NHB O–O nearest neighbors is ∼3.2 kcal/mol O–H ⋅⋅⋅ O or ∼6.4 kcal/mol H2O (13 kJ/mol O–H ⋅⋅⋅ O or 27 kJ/mol H2O). The NHB O–O nearest neighbors are held by forces other than those involving H ⋅⋅⋅ O partial covalency, i.e., electrostatic (multipole), induction, and dispersion forces. The NHB O–O pairs do not appear to produce significant intermolecular Raman intensity because they lack H ⋅⋅⋅O bond polarizability, but the corresponding NHB OH oscillators do contribute weakened Raman intensity above 3425 cm−1. An ideal solution thermodynamic treatment employing ΔH°1 =2.6 kcal/mol O–H ⋅⋅⋅ O, the HB mole fraction, and the vapor heat capacity, yielded a very satisfactory specific heat value of 1.1 cal deg−1 g−1 H2O at 0 °C. The NHB mole fraction, fu, from the YW treatment is negligibly small, 0.06 or less, for t<−50 °C. However, fu increases to 0.16 at 0 °C, and fu≊1 at 1437 °C, where recent shock-wave Raman measurements indicate loss of all partially covalent, charge transfer hydrogen bonding.

Potential constants for the hydrogen-bonded dimer H 2O⋯HF: Directional character of the hydrogen bond

Vibrational wavenumbers obtained from IR and microwave spectroscopy have been used to determine the hydrogen-bond stretching and in-plane bending potential energy constants for the dimer H 2O…HF in the quadratic approximation. The stretching force constants f s = 735 ± 10 Nm −t and f σ = 17.4 ± 0.3 Nm −1 are reported while the preferred set of in-plane bending force constants are f θ(i)θ(i) = 2.52 × 10 −20 J rad −2 and f φ(i)φ(i) = 19.70 × 10 −20 J rad −2, where θ(i) and φ(i) refer to bending at the oxygen and hydrogen atoms, respectively. This provides the second example of a gaseous hydrogen-bonded dimer for which it is concluded that a bent hydrogen bond is energetically unfavourable by comparison with a linear hydrogen bond. The relative ease of in-plane and out-of-plane distortions of the hydrogen bond are correlated with OH⋯O configurations determined in the solid state.

Hydrazonium(2+) hexafluorosilicate, N2H6SiF6: a NaCl-type structure with two-dimensional hydrogen-bonding networks

Hydrazonium(2+) hexafluorosilicate, N2H6SiF6, at room temperature has an orthorhombic (Pbca, Z = 4), pseudotetragonal unit cell (a = 7.605(1) Å, b = 7.586(2) Å, c = 8.543(1) Å). The structure consists of centrosymmetric N2H62+ and SiF62− ions arranged in a NaCl-type packing and connected by hydrogen bonds to two-dimensional N2H6–SiF6 layers parallel to (001). All H atoms are engaged in hydrogen bonding. Four of the six [Formula: see text] bonds to each cation are normal but significantly bent; the other two are trifurcated, [Formula: see text], but the out-of-layer component of the trifurcated bond is relatively unimportant. The N2H6SiF6 structure is compared in some detail with the structures of other hydrazonium(2+) salts, with particular attention to the N—N bond length, to the "effective" size of the N2H62+ ion, and to the tendency of this ion to form bent hydrogen bonds.

Structure and spectra of H2O in hydrated β-alumina

The structure and spectra of hydrated Li and Na β-alumina were investigated using neutron diffraction, infrared absorption, and Raman scattering. The dimensions of the hexagonal unit cell of a hydrated Li β-alumina crystal containing 1.55 H2O molecules per unit cell are a=5.591 Å and c=22.715 Å. The oxygen atoms of the water molecules are located in the conduction plane between the mO, and the aBR sites; the protons, located above the below the plane, form bent hydrogen bonds with the O(4) oxygen ions. The HOH bond angle of water in Li β-alumina is 114° and the ‖O–H‖ bond distance is 0.992 Å. Based on polarized infrared spectra, H2O adopts a similar structure and orientation in Na β-alumina. Spectra of absorbed H2O, D2O, and HDO species show that water molecules dissociate in Li β-alumina to form OH− and H(H2O)+n species. No evidence was found for the dissociation of water in Na β-alumina. The absorption coefficients determined for OH− and H2O in Li β-alumina include local field corrections. A large local field anisotropy at the protons of H2O is responsible for the large ratio of the intensities of ν3 and ν1 observed for water in Li and Na β-alumina.

Geometric relaxation in water. Its role in hydrophobic hydration

The thermodynamic quantities ΔG°, ΔH°, ΔS° and ΔC°p associated with the solvation of argon in water and aqueous mixtures are reinterpreted on the basis of two contributions. The first is related to the hydrogen-bonding connectivity of water and is assumed to be approximately represented by corresponding thermodynamic quantities in solvents such as hydrazine and ethylene glycol; following a proposal by Lumry and Frank [R. Lumry and H. S. Frank, Proc. 6th Int. Biophys. Congr.(1978), vol. 7, p. 554; R. Lumry, in Bioenergetics and Thermodynamics; Model Systems, ed. Y. Braibanti (Reidel, Dordrecht, 1980), p. 405] this contribution determines the free energy of hydrophobic hydration and is dominated by a positive enthalpy. The second contribution, which is responsible for marked enthalpy–entropy compensation and large heat-capacity effects in argon hydration, is assigned to the characteristic fluctuation behaviour of liquid water. This assignment is substantiated by comparisons of the bulk properties of water and various other liquids, and a model is suggested to rationalize the uncommon thermodynamic properties of water, aqueous mixtures and solutions of hydrophobic solutes. The phenomenological representation proposed is an overlay of a randomly connected H-bond network and a local fluctuation process defined in terms of a minimum cooperative unit. This process, labelled “geometric relaxation”, is pictured as a cooperative H-bond rearrangement involving a water molecule coordinated by four neighbours. The limiting microstates of the cooperative units are “short-bond” forms (with short, stiff, near-linear bonds) and “long-bond” forms (with long, weak, bent hydrogen bonds). The first is dominated by the low enthalpy of short hydrogen bonds and the second by the high entropy resulting from motions of the water molecules on flexible hydrogen bonds into the free volume not available to the “short-bond” form.

Bond-lengths, bond angles and transition barrier in ice Ih by neutron scattering

Although several studies1,2 of ordinary ice (Ih) have established its nearly perfect oxygen arrangement and the statistical distribution of hydrogen among two symmetrically equivalent sites (the ‘half-hydrogen’ model3), several fundamental problems remain. The O—H bond length found in ice Ih is considerably larger than in other polymorphs of ice determined precisely4,5, and many arguments have been put forward against the value observed5,6. Similarly, the tetrahedral H—O—H bond angle in ice Ih differs considerably from the value observed in the vapour phase, and this led Chidambaram7 to propose a bent hydrogen bond model which further splits the atom positions, and which has not yet been verified. Finally, the mean shape of the double potential governing the atom distribution and the barrier governing the mobility still remain to be evaluated. We show here how high-precision, short-wavelength neutron diffraction data from ice Ih can be used to evaluate the molecular structure and atomic density distribution at 60 K. The unusually long O—H distance is confirmed, but there is no evidence for bent hydrogen bonds. Indeed the hydrogen atom density distribution is well described by a librational motion of the hydrogen atom around the oxygen. The mean barrier height between the ‘half-hydrogen’ atom positions was obtained from the scattering density as 0.012 eV, which implies that the zero point motion is of high importance for the proton exchange at low temperatures.

Theoretical studies of hydrogen bonding in liquid water and dilute aqueous solutions

Monte Carlo computer simulations of liquid water and dilute aqueous solutions are analyzed in terms of the nature and extent of intermolecular hydrogen bonding. A geometric definition of the hydrogen bond is used. Calculations on liquid water at 25 °C, 37 °C, and 50 °C, were carried out based on the quantum mechanical MCY potential of Matsuoka, Clementi, and Yoshimine and at 10 °C based on the empirical ST2 potential. The effect of a dissolved solute on aqueous hydrogen bonding was studied for dilute aqueous solutions of Li+, Na+, K+, F−, Cl−, and CH4. The nature of the hydrogen bonding was characterized with quasicomponent distribution functions defined as a function of the intermolecular coordinates relevant to hydrogen bonding. The extent of the hydrogen bonding is described using a network analysis approach developed by Geiger, Stillinger, and Rahman. The results on the quasicomponent distribution functions show that the average hydrogen bond angle deviates with 10 °–25 ° from a linear form, quite independently of the potential function. The decrease in icelike character in liquid water as the temperature is increased is quantified. The structuration effects in solvent water for dilute aqueous solution of ionic and hydrophobic solutes are computed, and interpreted in terms of the Frank and Wen A, B and C regions of solvent. There is increased structure in the A region of both the ionic and apolar solutes, electrostrictive for the former and clathratelike for the latter. The B region is destructured in ionic solutions and shows increased icelike structural character in the solution of an apolar solute. The network analysis showed the existence of large space-filling hydrogen bonded networks. The occurrence of monomers was found to be negligibly small. These findings are in quantitative agreement with the analysis of molecular dynamics results by Geiger et al., based on an energetic hydrogen bond definition. Furthermore, the parameters of the distributions of the hydrogen bonded networks were found to be remarkably invariant to small change in the temperature, introduction of a solute and the change of the potential function. The average cluster size and related parameters are quite sensitive to the number of molecules considered. Overall, the analysis supports the validity of viewing liquid water in terms of a Pople continuum and Sceats–Rice random network model of water molecules interacting mainly via bent hydrogen bonds.

The structure and ir spectroscopic behaviour of phthalazine hemiperchlorate

X-ray diffraction studies reveal that in phthalazine hemiperchlorate there are short, asymmetric [NH·N] −1, slightly bent hydrogen bonds, the N·N distance being 2.656(16) Å. The anomalous temperature effect in the far infrared absorption is also observed in this case. Numerous Evans holes can be assigned to skeletal distortion modes.

Ab initio LCMO studies on the hydration of formate ion

Ab initio calculations on the formate water complex in different intermolecular orientations are reported. The intermolecular distance was optimized at frozen subunit geometries. The most stable arrangement is a cyclic heterodimer with two bent hydrogen bonds ( R CO = 3.23 A, Δ E = -19.3 kcal/mole.

A zeroth order random network model of liquid water

A random network model is used to generate the oxygen–oxygen pair correlation function of liquid water and amorphous solid water. The model is basically an extension of the bent hydrogen bond model proposed by Pople in 1951; it differs from the earlier work in that instead of being a parametric fit to the data, it predicts the dispersion in OO distances for each shell of neighbors, and the dispersion in OOO angles, from independent spectroscopic data. Our random network model is based on the hypothesis that there exists a separation of time scales for various classes of molecular motion in liquid water. In particular we assert that it is useful to regard libration and hindered translation as occurring in a quasistatic network of bonded molecules and diffusion and related relaxation processes as occurring much more slowly. The predicted OO pair correlation function is in good but not perfect agreement with experiment over a wide temperature range. As a further test the model is used to predict the dielectric constant of liquid water. Excellent agreement is found over the temperature range 10–300 °C. The relationship between the random network model and computer simulations of liquid water is extensively discussed.