Showing papers on "Hydrogen bond published in 1971"
TL;DR: In this article, the most stable conformation has an O···H distance of 1.89 A with
Abstract: Ab initio LCAO–MO–SCF calculation for H2CO···H2O is carried out with a minimal Slater basis set. The most stable conformation has an O···H distance of 1.89 A with
1,608 citations
TL;DR: In this paper, it was shown that only slight changes in rotation occur on changing the solvent for conformationally rigid molecules, and the magnitude of the anomeric effect was influenced as expected by changes in the polarity of the solvent but hydrogen bonding with the acetal oxygen atoms had a more pronounced effect.
Abstract: The empirical rules for estimating molar rotations of carbohydrate structures proposed by Whiffen and elaborated by Brewster provided interpretations of solvent effects on optical rotation with changes in conformational equilibria which in certain cases were confirmed by n.m.r. Conversely, it was found that only slight changes in rotation occur on changing the solvent for conformationally rigid molecules. Thus, studies involving optical rotations measured at the D-line of sodium and n.m.r. spectra provided the experimental support for the following solvation phenomena which are related to the role of unshared pairs of electrons in conformational equilibria. (a) The reverse anomeric effect was substantiated by the effect of introducing a positive charge on the imidazole ring of certain N-glycosides of imidazole. (b) The magnitude of the anomeric effect was influenced as expected by changes in the polarity of the solvent but hydrogen bonding of the solvent with the acetal oxygen atoms had a more pronounced effect. (c) The orientation of oxygen atoms in gauche relationship appears particularly favourable with water as solvent. (d) An intramolecular hydrogen bond between two hydroxyl groups is strengthened by hydrogen bonding of the free hydrogen to a basic solvent. le) The non-bonded interaction between two opposing axial oxygen atoms is dependent on the nature of the substituents. The repulsion is substantially greater when the oxygen atoms are either bonded to methyl groups or hydrogen-bonded to the solvent than when attached to acetyl, benzoyl or methane-sulphonyl groups. Tim first statement that unshared pairs of electrons may play an important role in establishing conformational preferences was made by Edward' with reference to the apparent stability of that anomeric form for a glycosyl halide which has the halogen in axial orientation. The statement made was, as seen in Figure 1, that by going axial the polar C, to X bond avoids an interaction with the axially oriented orbital of the ring oxygen. Later this was discussed by Kabayama and Patterson2 who pointed out that the unfavourable interactions could, indeed, involve repulsions between the orbitals occupied by lone pairs of electrons in the aglycon X with those of the ring oxygen. Such interactions equivalent to syn-axial interactions, would be released on passing from the equatorial to axial anomer.
285 citations
TL;DR: In this paper, the presence or absence of a double-well potential depends on the repulsive or attractive nature of the A−H1 and H1−B potentials, depending on the relative position of the molecular fragments A and B, and on the attractive or repulsive interaction of the fragments B and A. In particular, it is suggested to use the designation "hydrogen bridge" as a more general designation for what is commonly referred to as hydrogen bond.
Abstract: In this work we analyze molecular complexes with two hydrogen bonds (A=H2=B) and with three hydrogen bonds (A≡H3≡B). In an introductory discussion of molecular complexes with a single hydrogen bond (A–H1–B), it is argued that the presence or absence of a double‐well potential depends primarily on (a) the repulsive or attractive nature of the A–H1 and H1–B potentials, (b) on the relative position of the molecular fragments A and B, (c) on the attractive or repulsive interaction of the fragments A and B. Since the A–H1–B complex can be stable if one of the potentials for A–H1 or H1–B is repulsive, provided that the attraction of A and B compensates the above repulsions, it is suggested to use the designation “hydrogen bridge” as a more general designation for what is commonly referred to as “hydrogen bond.” The guanine–cytosine (G–C) base pair is taken as an example of three hydrogen bridges (h–b's). A number of computations were performed to assess the shape of the potential curve for the h–b in the G–C pa...
196 citations
TL;DR: The positions of the five hydrogen atoms in the mineral brushite, CaHPO4,2H2O, which crystallizes with Z = 4 in the non-centrosymmetric monoclinic space group la(Cs4), have been established by neutron-diffraction analysis based on 632 independent reflexions from synthetic crystals as mentioned in this paper.
Abstract: The positions of the five crystallographically independent hydrogen atoms in the mineral brushite, CaHPO4,2H2O, which crystallizes with Z= 4 in the non-centrosymmetric monoclinic space group la(Cs4), have been established by neutron-diffraction analysis based on 632 independent reflexions from synthetic crystals. Anisotropic three-dimensional least-squares refinement of all the atoms in the structure to R 0·033 gives final estimated standard deviations of 0·002 for calcium ions, ca. 0·006 for phosphorus and oxygen atoms, and 0·010–0·015 A for hydrogen atoms. The final Fourier difference synthesis shows no significant spurious peaks and there is no evidence that any hydrogen atom occupies several sites; the anionic hydrogen is 1·00(1)A from O(1), which has the longest [1·608(6)A] P–O bond. The two water molecules co-ordinate somewhat differently; both are essentially coplanar with the oxygen atoms to which they are hydrogen bonded, but water (2) has an unusually long bond of 3·09 A to water (1). The other four distinct hydrogen bonds in the structure, which closely resembles that of the arsenic analogue, pharmacolite, have O ⋯ O lengths ranging from 2·68 to 2·83 A.
188 citations
TL;DR: In this paper, the electron diffraction patterns of gaseous acetic acid at 160 °C for the monomer and at 24 °C to obtain the molecular geometry were obtained (first value for monomer, second for dimer, standard deviations in parentheses).
171 citations
TL;DR: In this paper, a study has been made of the infrared O-H bands for CH3OH, DOH, and H2O in solution and of their correlation with hydrogen bonding and solvent basicity.
Abstract: A study has been made of the infrared O—H bands for CH3OH, DOH, and H2O in solution and of their correlation with hydrogen bonding and solvent basicity. Infrared bands for the three fundamentals an...
144 citations
TL;DR: In this article, the stretching vibrations of water in montmorillonite, hectorite, saponite and vermiculite are split into two components, similar to those seen in perchlorate solutions.
Abstract: The stretching vibrations of water (H2O, HDO and D2O) in montmorillonite, hectorite, saponite and vermiculite are split into two components, similar to those seen in perchlorate solutions. Examination of lower hydrates and pyridine complexes of the layer silicates shows that the higher frequency component corresponds to hydrogen bonds to oxygens of Si—O—Si linkages, the lower frequency component to water-water bonds and hydrogen bonds to oxygens of Al—O—Si linkages. The observations are explained in terms of chains of hydrogen-bonded water molecules which form dielectric links between interlayer cations and oxygens on the silicate anion surface. This concept, together with information obtained on the distribution of charge on the surface oxygens, provides a qualitative explanation of the hydration properties of layer silicates, and is extended to account for the stability of organic complexes of montmorillonite and hectorite. Some analogies between interlayer complexes and ionic solutions are proposed.
141 citations
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122 citations
TL;DR: In general, physical and chemical results, as well as the base homologies in different tRNA molecules, support Holley's “clover leaf” model and it should be possible to determine molecular conformations in solution by studying the hydrogen bonds directly.
Abstract: SINCE the determination of their primary sequence the secondary and tertiary structures of tRNA molecules have been studied by various techniques (reviewed in ref. 1). In general, physical and chemical results, as well as the base homologies in different tRNA molecules, support Holley's “clover leaf” model2. There is also evidence of tertiary structure, and different models have been suggested3. Because both secondary and tertiary structures depend on hydrogen bonding, it should be possible to determine molecular conformations in solution by studying the hydrogen bonds directly.
TL;DR: In this paper, a geometry search restricted to structures with linear and bifurcated hydrogen bonds is performed and the associated potential energy curves are displayed, and the minimum energy geometry of the water dimer is found to form a linear hydrogen bond with a hydrogen bond distance of 2.04 A and a binding energy of 4.84 kcal/mole relative to the monomer.
Abstract: The hydrogen bond in the water dimer is studied within the SCF-MO-LCAO framework, using a large Gaussian basis set to approximate the wavefunction. A geometry search restricted to structures with linear and bifurcated hydrogen bonds is performed and the associated potential energy curves are displayed. The minimum energy geometry of the water dimer is found to form a linear hydrogen bond with a hydrogen bond distance of 2.04 A and a binding energy of 4.84 kcal/mole relative to the monomer (exp. 5.0 kcal/mole). No semistable structures are found. The charge density and charge density difference maps are discussed for the structure with a linear hydrogen bond for different subsystem (water) separations, including the minimum energy geometry. The dipole moment of the dimer is computed to be 1.69 a.u. The shift of the IR bands on hydrogen bond formation is explained qualitatively by comparing the potential energy curves of the hydrogen in the OH-bonds of the monomer and the dimer, and the intensity increase of the fundamental OH-stretching band is computed. The shift of the proton magnetic resonance signal is discussed qualitatively by inspecting the charge density change on hydrogen bond formation, and the average diamagnetic shielding is calculated.
TL;DR: In this paper, minimal basis LCAOSCF molecular orbital calculations have been performed on open chain dimers and trimers containing methanol and water, and the equilibrium structures and energies of the dimers are determined and compared.
Abstract: Ab initio minimal basis LCAOSCF molecular orbital calculations have been performed on open chain dimers and trimers containing methanol and water. The equilibrium structures and energies of the dimers are determined and compared. The rigidity of the hydrogen bond in each dimer is discussed in terms of calculated intermolecular force constants. The energies of seven open chain trimers are presented and analyzed. It is found that the energies of all trimers deviate from additivity, indicating the existence of a cooperative effect in hydrogen bonding in these systems.
TL;DR: The three-dimensional structure of the disodium salt of adenosine triphosphate (Na 2 ATP) has been determined from an X-ray diffraction study to a resolution of 0.9 A as discussed by the authors.
Abstract: The three-dimensional structure of the hydrated disodium salt of adenosine triphosphate (Na 2 ATP) has been determined from an X-ray diffraction study to a resolution of 0.9 A. The crystals are orthorhombic, space group P 2 1 2 1 2 1 , with a = 30.45(4), b = 20.88(3), c = 7.07(1) A. There are two molecules of ATP, four sodium ions, and six water molecules in the asymmetric unit. The structure was solved by direct methods and refined to R = 12.3 % using 1118 intensities measured on an automatic diffractometer. The triphosphate chain is in the folded conformation in each of the two crystallographically independent molecules. However, in one molecule (A) it is folded so as to form part of a lefthanded helix, while in the other part of a right-handed helix. There are corresponding differences in the conformations of the ribose rings. The ring is in the envelope conformation with C39 endo in molecule A and C29 endo in molecule B. Two of the sodium ions coordinate the two molecules through the phosphate oxygens and N7 to form an almost centrosymmetric ‘dimer’ which is the fundamental structural unit. The adenine bases show considerable overlap and are stacked in the c axis direction. Details of the hydrogen bonding and the role of water molecules in the structure are discussed.
TL;DR: Coupled hydrogen bond systems have been shown to be interesting subjects of further research as discussed by the authors, for example, in ice, liquid water, hydroquinone clathrates, starch, cellulose, polypeptides, nucleic acids, and silicate hydrates.
Abstract: The “hydrogen bond” or “hydrogen bridge” concept has proved to be one of the most useful structural concepts in modern science. The properties of substances containing hydrogen bonds depend on the strength, symmetry, and polarity of these bonds. These characteristics, in turn, are related to the effective electronegativities of the bridgehead atoms, the distance between these atoms, and the degree of coupling with other hydrogen bonds. Symmetrical hydrogen bonds exist in the FHF− and H5O ions and in some acidic compounds. Coupled hydrogen bond systems exist, for example, in ice, liquid water, hydroquinone clathrates, starch, cellulose, polypeptides, nucleic acids, KH2PO4, and silicate hydrates. It is suggested that systems of coupled, nearly symmetrical, hydrogen bonds should be interesting subjects of further research.
TL;DR: In this article, the bending force constants of the gas phase complexes HCN-HF, DCN-DF and four isotopic species of CH$3}$CN-HF have been measured over the range 200 to 4000 cm$-1}$.
Abstract: The infrared spectra of the gas phase complexes HCN-HF, DCN-DF and four isotopic species of CH$_{3}$CN-HF have been measured over the range 200 to 4000 cm$^{-1}$. Two bands have been observed, one associated with the stretching vibration of HF in the complex and the other with a bending vibration of the hydrogen bond itself. At higher resolution both bands show fine structure which has been interpreted as being a series of hot bands associated with transitions from excited levels of another low-frequency bending vibration of the hydrogen bond. In the first band the peaks are P branch bandheads in the individual hot bands and in the second band they are sharp Q branches. From temperature studies of these bands and from the effects of isotopic substitution on the spacing of the fine structure the frequency of the lower bending vibration has been determined. Further structure in the first band gives the frequency of the stretching vibration of the hydrogen bond itself. A complete assignment of all the vibrations associated with the hydrogen bond has therefore been made. From the frequencies of the two bending motions (555 and 70 cm$^{-1}$ for the HCN-HF complex) values of the bending force constants have been calculated. Several anharmonic constants have also been measured and the effect of anharmonicity on the breadth of bands associated with the hydrogen bond is discussed.
TL;DR: The crystal structure of D-glucitol, C6H1406, A form, from ethanol solution, has been determined from three-dimensional X-ray and neutron diffractometer data as discussed by the authors.
Abstract: The crystal structure of D-glucitol, C6H1406, A form, from ethanol solution, has been determined from three-dimensional X-ray and neutron diffractometer data. The structure was solved by direct methods using the Karle & Hauptman tangent formula, and refined anisotropically to an R value of 0-032 for the X-ray data and to R= 0.066 for the neutron data. The space group is P212121, Z= 4, a= 8"677 (5) b=9-311 (8), c=9.727 (4)/~, D x = 1-541, Dm= 1"535 g.cm -3. The molecule has the bent chain conformation, with C(1) 1.06 A out of the plane of the other five carbon atoms, which are coplanar within + 0.01/~. The C-C bond lengths are normal, with a mean value of 1.520 A. The molecules stack with their chain axes approximately parallel, as is usual with the alditols. Each hydroxyl group is involved in two hydrogen bonds. These bonds form two infinite spirals, one linking the odd-numbered oxygen atoms in the e direction and the other linking the even-numbered oxygens in the a direction. There is an unexpected and unexplained systematic distinction between these chains in the OH. . .O hydrogen bond separations, the former ranging from 1"91 to 2.22/~ and the latter from 1 "69 to 1.73/~. The corresponding O-(H). . .O separations are 2"88 to 3-17 A and 2.65 to 2.68 A. Because of this unusual feature of the intermolecular hydrogen bonding, which has not been observed in other alditol structures, the X-ray data collection was repeated, although the first data yielded an R= 0.04. The final parameters are all within 3o" of those from the first set of data. The neutron data confirmed the heavy atom positions and gave more precise parameters for the hydrogens.
TL;DR: The high resolution nuclear magnetic resonance spectra of hydrogen bonded protons in four purified tRNA molecules are reported and it is shown that these resonances arise from intramolecular hydrogen bonds.
TL;DR: In this article, a neutron diffraction study of bis(2.amino−2.methyl−3.butanone oximato)nickel(II) chloride monohydrate {Ni(C5H11N2O)2H}+Cl−·H2O has provided a wealth of precise information concerning the short intramolecular hydrogen bond, the dynamics of rotating methyl groups, and the effects of intermolecular environment on potential functions.
Abstract: A neutron diffraction study of bis(2‐amino‐2‐methyl‐3‐butanone oximato)nickel(II) chloride monohydrate {Ni(C5H11N2O)2H}+Cl−·H2O has provided a wealth of precise information concerning the short intramolecular hydrogen bond, the dynamics of rotating methyl groups, and the effects of intermolecular environment on potential functions. The intensities of 3500 single‐crystal reflections were measured at the Brookhaven High Flux Beam Reactor. These data were used in conjunction with the earlier x‐ray determination to locate all atoms including the 25 hydrogen atoms. After least squares refinement with anisotropic temperature factors, the agreement factor R = ΣΔ(F2) / ΣF02 was 0.055. The short intramolecular hydrogen bond O···O [2.420(3) A] is unique in that no bond symmetry is imposed by the space group, and it is slightly asymmetrical. The O–H bond lengths for the hydrogen bond are 1.242(5) and 1.187(5) A, and the O–H–O angle is 169.9(3)°. The potential apparently has a broad, flat, single minimum, shifted tow...
TL;DR: From the present results it appears that the tetrameric base arrangement of Gellert et al [2] is highly probable, but a priori no need for the continuous helix exists.
TL;DR: A three dimensional structure of the antamanide·Na+ complex has been proposed containing four intramolecular hydrogen bonds formed by the amide CO and NH groups, which explains the efficiency and selectivity of theantamanide complexation reaction.
TL;DR: In this article, the electron diffraction patterns of gaseous propionic acid were obtained and the following parameters for the molecular geometry were obtained (first value for monomer, second for dimer, standard deviations in parentheses): C 1 -C 2 : 1.518 (0.010), 1.543(0.015) A C 2 -C 3 :1.547 ( 0.003), l.
TL;DR: In this paper, small polar organic molecules are separated from one another on Sephadex LH-20 Modified Dextran either by sieving or by adsorption through π or hydrogen bonds.
TL;DR: Extended Huckel theory has been used to calculate the torsional angles for the sugar phosphate bonds which lead to stable conformations and it appears that in a double helical structure, the nonbonded and “stacking” interactions provide the stability to the conformational structure of each strand.
TL;DR: In this article, the authors defined the fractional coordinates of atoms from planes and the positions of atoms in the planes of the planes, where X, Y, Z are fractional coordinate coordinates.
Abstract: J= 1 3\"889X-4\"193 Y+ 7\"IO5Z= 3\"639 J = 2 5\"079X+9\"583Y-4\"700Z=5.589 J = 3 4\"573X+ 9\"943 Y 3-692Z= 6\"765 X, Y, Z are fractional coordinates Displacements of atoms from planes J = l J = 2 J=3 C(J1) 0.003 • -0.002 .~, -0.006 C(J2) 0.007 0-001 0.002 C(J 3) 0.008 0.000 0.003 C(J4) 0\"001 0\"001 0\"004 C(J5) 0.011 -0.001 -0-000 C(J6) -0.011 0.001 0.005 C(J7) -0.062 0.023 0-050 C(J8) -0.025 -0.093 0.115 O(Jl) 0.021 -0.010 -0.034 N(J 1 ) 0\" 173 0-153 0.033 Cu -0.239 0.368 -0.109
TL;DR: The alternating polydeoxynucleotide poly with 4-thiothymidine substituting for thymidine shows anomalous spectral and hydrodynamic properties which are inconsistent with a Watson-Crick structure but agree with a model of a left-handed double helix built up from Haschemeyer-Sobell (reversed Hoogsteen) base-pairs instead.
Abstract: The alternating polydeoxynucleotide poly[d(A-s4T) · d(A-s4T)] with 4-thiothymidine substituting for thymidine shows anomalous spectral and hydrodynamic properties which are inconsistent with a Watson-Crick structure but agree with a model of a left-handed double helix built up from Haschemeyer-Sobell (reversed Hoogsteen) base-pairs instead.
Optical-rotatory-dispersion and circular-dichroism spectra exhibit a strong negative Cotton effect centered near 400 nm that is assigned to a nπ* transition of the thioamide chromophor and that is at least unexpected if the sulfur atom participates in the hydrogen bridge. From the inversion of the Cotton effects between 370 and 400 nm with respect to the monomer or randomcoil state it is inferred that 4-thiothymidine attains the unusual syn conformation in the ordered polymer. At pH below 4.5 the polymer is protonated at N-1 of the deoxyadenosine residues and changes into a different helical conformation. As the inflection point of the proton-induced transition falls close to the basic pK of deoxyadenosine monophosphate, also N-1 (A) is probably not involved in hydrogen bonding. Therefore, only N-7 (A) and 0-2 (s4T) remain as proton acceptors for base-pairing.
The polymer undergoes cooperative temperature-dependent transitions in concentrated solutions of 1:1 electrolytes. Two more helical conformations are characterized by ultraviolet, optical-rotatory dispersion, and circular dichroism. In addition, changes in hydrodynamic parameters, e.g. sedimentation coefficient, buoyant density and partial specific-volume are reported. A structural hysteresis is observed in a helix-helix transition and is discussed in terms of metastable states indicated from a phase diagram.