Positions Of Hydrogen Atoms Research Articles

Crystal structure of cyanoacetamide

Crystals of cyanoacetamide, NCCH2CONH2, are monoclinic, space group P21/c, a= 8·36, b= 13·56, c= 7·56 Å, β= 111·2°, Z= 8 (two molecules in the asymmetric unit). The structure was determined with Cu-Kα scintillation counter data from Patterson and electron-density maps, and refined by least-squares methods to R 0·089 for 1129 observed reflexions. Hydrogen atom positions were determined from a difference synthesis.

Crystal structure of malonamide

Crystals of malonamide, CH2(CONH2)2, are monoclinic, space group P21/c, a= 13·07, b= 9·45, c= 8·04 A, β= 73·0°, Z= 8 (two molecules in the asymmetric unit). The structure was determined with Mo-Kα diffractometer data by the symbolic addition procedure, and refined by least-squares methods, to R 0·05 for 941 observed reflexions. Hydrogen atom positions were determined.The two symmetry-unrelated molecules have different orientations in the crystal, but have similar conformations and dimensions. The amide groups are rotated out of the central CCC plane, one group in each molecule by about 65°, and the other group by 40°. The mean bond distances, after applying rotational oscillation corrections, are C–C 1·507, C–N 1·334, C–O 1·253 A(σ 0·004 A); there are no significant deviations from these mean values. The molecules are held together by a system of eight N–H ⋯ O hydrogen bonds (2·89–3·14 A) involving all the amino-hydrogen atoms, with each oxygen atom acting as an acceptor in two hydrogen bonds.

Crystal and molecular structure of 2,6-dimethyl-4-phenylphosphorin

The structure of 2,6-dimethyl-4-phenylphosphorin, C13H13P, has been determined by single-crystal X-ray methods. The space group is P212121 with a= 7·312(5), b= 14·333(7), and c= 10·820(8)Å. The intensities of 935 planes, measured on a linear diffractometer; the final R was 0·052. Hydrogen-atom positions were located. The molecule possesses an approximate two-fold symmetry axis and the two planar six-membered rings have a dihedral angle of 38·6°. Phosphorin is the phosphorus analogue of pyridine and the planar C5P ring has two equal phosphorus–carbon bond-lengths of 1·743(5)Å, and four equal carbon–carbon bond-lengths [mean 1·388(9)Å]. The CPC angle is 102·4(2)°.

O—H … S Hydrogen Bond in Barium Thiosulphate Monohydrate

THERE is evidence that the sulphur atom is capable of participating in hydrogen bonding systems in solids1–3, and numerous diffraction studies suggest that a few different types of this hydrogen bond may exist. Most of these studies are concerned, however, only with interatomic distances and angles involving the donor and acceptor atoms, and the position of the hydrogen atom has been determined in only a small number of cases. The type of X—H … S bond which is best known is that with X=N, and it has been shown by neutron diffraction that such bonds are present in, for example, both room and low temperature forms of thiourea4. The crystallo-chemistry of solid H2S (ref. 5) led Hamilton and Ibers3 to believe that the S—H … S bond also occurs. Finally, the crystal structures of magnesium thiosulphate hexahydrate6, barium thiosulphate monohydrate7 and 4,4′dihydroxythiobenzophenone monohydrate8, for example, indicate that the O—H … S bond may also exist, but these compounds were studied by X-ray methods in which the position of the hydrogen atom could not be determined. Further evidence is required to confirm the existence of the O—H … S bond in solids.

The crystal structure of the zeolite hydrogen faujasite

Recent infrared studies of the hydroxyl groups in hydrogen faujasite-type zeolites indicate that there are two acidic, catalytically reactive -OH groups in this structure. These studies also indicate that the two groups have different acidic strengths and are not equally accessible to incoming molecules. Using single-crystal X-ray techniques, we have determined the crystal structure of H faujasite (calcined, ammonium-exchanged natural faujasite). The hydrogen atom positions were not determined directly, but were deduced from the four independent Si(Al)O distances. In our model, the hydrogen atoms are bonded to two of the four unique groups of oxygen atoms inherent in the disordered faujasite model. One of the H-atom positions is in the hexagonal prism and the other is on the highly accessible bridging, hexagonal prism oxygen atom. Electrostatic field calculations imply that this model would give rise to two unique IR -OH bands. The model also agrees with the Si,Al ordering scheme proposed earlier for faujasite-type zeolites.

Hydrogen atom positions in manganous formate dihydrate and a rerefinement of copper formate dihydrate

Hydrogen atom positions in manganous formate dihydrate and a rerefinement of copper formate dihydrate

Recent research on polymer structure

Abstract

Structure of Cubic Ammonium Fluosilicate: Neutron-Diffraction and Neutron-Inelastic-Scattering Studies

The motion of the ammonium ion in the cubic phase of (NH4)2SiF6 has been investigated by the inelastic scattering of slow neutrons. The prominent feature of the neutron energy-gain spectrum is a moderately broad band peaked at 168±8 cm−1 with a shoulder at 305±25 cm−1. These are assigned to the 1–0 and 2–0 transitions of a rotational motion of the ammonium ion. A precision refinement of single-crystal neuron-diffraction data has also been completed. There is a well-defined disorder of the ammonium groups. Although a model with a static threefold disorder, with each ⅓ hydrogen atom undergoing harmonic vibration gives a very satisfactory fit to the data, such a model is probably unrealistic in view of the fact that the disordered positions are only 0.75 Å apart. A more realistic model is one involving an ordered hydrogen atom undergoing thermal motion in a very anharmonic potential well. We propose a model in which the hydrogen atom is relatively free to move over a region of about 1 Å2 by small rotations of the ammonium ion but with a very high barrier toward a reorientation which involves an interchange of two hydrogen atoms. Such a model is an agreement with both the neutron-diffraction and the inelastic-scattering data. The hydrogen-atom positions found in the diffraction study do not agree with those reported by Vainshtein on the basis of an analysis of the electron-diffraction data. The N–H bond length is not well defined because of the uncertainties regarding the thermal motion. An uncorrected mean atomic separation of 0.985 (σ=0.007) is obtained; the actual bond length is about 0.08 Å longer. The SiF62— ion is a regular octahedron with a corrected bond length Si–F=1.696 (σ=0.003).

Hydrogen and deuterium atom abstraction from methanol and trideuteromethanol. Reaction of methoxy radicals with methane

The reactions of trideuteromethyl radicals with methanol and trideuteromethanol have been studied in order to determine the position and rate of hydrogen and deuterium atom abstraction. Over the temperature range studied (130–250°C) the rate of abstraction from the methyl and hydroxyl groups is similar. Substitution of deuterium for hydrogen alters the positional reactivity by an amount in agreement with zero-point energy difference. Rate constants at 182°C and Arrhenius parameters (based on a value of 1013.34mole–1cm3sec–1 for the recombination rate constant of methyl radicals) have been measured for the reactions:[graphic omitted] and have been calculated for [graphic omitted]Units k and A mole–1 cm3 sec–1, E kcal mole–1.

Nuclear Magnetic Resonance Studies Concerning the Effect of Adjacent Hydrogen Atoms on the Hydrogen-Bond Properties

The proton-resonance absorption spectrum has been studied in several hydrogen-bonded solids with different O–H···O bond lengths ranging from 2.45 to 3.30 Å. The resonance linewidth increases with the O–H···O bond length and shows a tendency to flatten out when the bond length exceeds 2.72 Å. The proton-resonance absorption linewidth in molecular solids is due primarily to nuclear dipole—dipole interaction, and hence it is proportional to Σk(rjk)—3, where rjk is the distance between Protons j and k, where j is any particular chosen proton. Because of the inverse-cube dependence on r, appreciable contribution to the line broadening comes from nearest neighbors only. The dependence of the proton-resonance linewidth on the hydrogen-bond length, therefore, points out that the hydrogen-bond length gets smaller when the protons are far apart and larger when they are close. This result was verified independently by calculating the nearest hydrogen—hydrogen distances for compounds where the positions of hydrogen atoms are known from neutron-diffraction studies and in other cases by estimating these distances from the usual values of the bond lengths and bond angles. The observed result is explained by postulating that the interaction between the two O–H bonds involved in two adjacent O–H···O bonds is essentially electrostatic in origin; the interaction potential consists of attractive terms due to dipole—dipole, induced dipole, and dispersion interactions in addition to a repulsive term. The calculated interaction energy between two O–H···O hydrogen bonds is attractive up to O–H···O bond lengths of 2.80 Å and has a minimum value around 2.70 Å. The O–H···O bond length of 2.70 Å seems to be most preferred from the point of view of this energy. This is consistent with the fact that there are a large number of hydrogen-bonded solids with bond lengths around 2.70 Å.

Crystal Structure of Cerium Magnesium Nitrate Hydrate

According to single-crystal x-ray diffraction data, crystals of Ce2Mg3(NO3)12·24H2O are rhombohedral, space group R3̄. The hexagonal cell with a = 11.004±0.006, c = 34.592±0.012 Å contains three formula units. Atomic parameters were refined by least squares, and interatomic distances were corrected for thermal motion. The average N–O bond distance in nitrate is 1.26 Å. The Ce atoms, on the threefold axis at z = ±0.2497, are each surrounded by 12 oxygen atoms at an average distance of 2.64 Å. These oxygen atoms, belonging to six nitrate ions, are at the corners of a somewhat irregular icosahedron. The Mg atoms are of two kinds, located, respectively, at the origin and on the threefold axis at z = ±0.4279. Each Mg atom is surrounded by six water molecules with the oxygen atoms at the corners of an octahedron with an average Mg–O distance of 2.07 Å. One-fourth of the water molecules are not coordinated to cations. Evidence for the hydrogen atom positions from the diffraction data indicates that six of the eight independent hydrogen atoms are involved in normal hydrogen bonds.

Enhancement of Fluorescence Yield of Rare-Earth Ions by Heavy Water

Experiments on the fluorescence yield of rare earth ions showed that the substitution of deuterated water for ordinary piotonated water markedly increases the light yield in most cases. The effect seems to be inversely dependent upon the energy gap between the highest level of the ground multiplet and the resonance level of the rare earth ion from which emission occurs. Thus, the order of magnitude of change of emission intensity is Eu/sup 3+/ > Tb/sup 3+/ > Gd/sup 3+/, while the energy gaps between the resonance level and the high-lying ground level for the same ions are 12 300, 14 200, and 32 100 cm/sup -1/, respectively. (P.C.H.) nated to cations. Evidence for the hydrogen atom positions

The structure of vitamin B 12 III. The crystal structure analysis of the air-dried B 12 crystals

The X-ray structure analysis of vitamin B 12 in the air-dried crystals is described in detail up to the point at which the molecular structure was considered established apart from certain double bond and hydrogen atom positions. The heavy-atom technique was used, based on the cobalt atom which is an intrinsic part of the B 12 molecule. While this atom was much more effective in phase determination than a formal calculation of its scattering power as against that of the rest of the crystal asymmetric unit would indicate, it was not a sufficiently dominating influence, and consequently the electron density maps based on cobalt phases alone contained too many spurious peaks for a complete structure to be postulated at the initial stage. Some form of trial was therefore necessary; this took the form of comparing the densities generated by several rather different postulated scattering nuclei included in the phase calculations. The techniques by which the very strong bias towards atoms inserted in the calculations in the non-centrosymmetric case could be circumvented are described, as are other aspects of the work which have a bearing on future structure analyses of very complex organic molecules.

The structure of vitamin B 12 V. The structure of the air-dried crystals of vitamin B 12

The refinement of the positions found in air-dried B 12 crystals in the Oxford and Princeton investigations has been carried out through four cycles of structure factor and electron density calculations, on the basis of the Princeton data. Owing to the disordered character of the dried crystal and consequent limitations on the X-ray data, no high precision of atom placing can be achieved; preferred parameters are listed for 93 atoms of the B 12 molecule and 15 water molecules with an additional 7 less well-defined water molecule sites. Certain interesting features of molecular geometry have appeared during structure refinement. The two planes of the benziminazole ring and inner atoms of the corrin nucleus, around which the molecule is constructed, lie at an angle of 80° to one another—the angle of tilt seems to be required by the close contact between the benziminazole nitrogen atom and the methyl group attached at the direct junction between two of the five-membered rings of the corrin nucleus. The projected position of the benziminazole ring across the nucleus also seems to be determined largely by packing considerations within the molecule; various small distortions occur which increase otherwise too short contacts. The latest difference density maps somewhat strengthen the identification as methyl groups of the various single atom substituents to the nucleus; they show small peaks at many of the possible hydrogen atom positions. Of the 18 water molecules indicated by the crystal density, the major part are in definite positions, hydrogen bonded to one another and to active groups on the molecular surface, the remainder are somewhat disordered by the crystal drying and are probably stranded at different positions in different unit cells, among the possible sites listed.

Molecular Structure of B9H13(CH3CN)

A three-dimensional x-ray diffraction study of a single crystal of B9H13(CH3CN) has yielded the complete structure, including hydrogen atom positions. The nine boron atoms form an icosahedral fragment, like the arrangement in B10H14 with one boron atom missing. The structure is consistent with the present form of the topological theory of boron hydrides and ions in that it has two BH2 groups, and is related to an anticipated B9H14— ion in the same way that B10H12(CH3CN)2 is related to B10H14—2 ion. The crystals are monoclinic, in the space group P21/m, and have two molecules in a unit cell having parameters a=5.64, b=9.22, c=9.81 A and β=90°±30 min.

Electron Diffraction Investigation on the Molecular Structure of n-Butane

Abstract The molecular structure of n-butane has been investigated by means of the sector-microphotometer method of electron diffraction. The least-square analysis of the radial distribution curve has been carried out both for modified and unmodified curves giving the internuclear distances as well as their mean amplitudes and the bond angles. The estimation of experimental standard errors has been made by examining various sources of errors. Important results are the following: a) The average distance of the C–C bonds is 1.539±0.003Å. b) The angle C–C–C is 112°9′± 9′, is considerably greater than the tetrahedral angle. c) The position of hydrogen atoms is located with considerable accuracy; C–H=1.100±0.003Å and <C–C–H=110°22′±15′. d) The mean amplitudes measured are in agreement with the calculated values within the limit of error. e) The existence of rotational isomers, the trans and the gauche forms, are confirmed. The structure and the fraction of the isomers are determined. The result is consistent with the spectroscopic results.

Least Squares Refinements of B10H14, B4H10, and B5H11

New interatomic distances in B10H14, B4H10, and B5H11 indicate that the B–B distances which are more strongly bound in the simplified valence theory are slightly shorter than other B–B distances. The position of the unique hydrogen atom in B5H11 is now somewhat more satisfactory in relation to the plane of symmetry of the isolated molecule. The improvement of agreement of observed and calculated x-ray intensities suggests that least squares refinements as usually applied are not carried through enough iterations.

The positions of hydrogen atoms in urea by neutron diffraction

The positions of hydrogen atoms in urea by neutron diffraction

Electron Diffraction Study of the Hydrogen Bonds in Boric Acid

IN recent years the techniques of X-ray diffraction structure analysis have been refined to such an extent that, with careful work, the positions of hydrogen atoms in a structure may be determined when each hydrogen atom is bound to a single atom. The detection of a hydrogen ion in a hydrogen bond, however, is a much more difficult task, since only a fraction of an electron can be considered as localized near the proton. This amount of ionization reduces the atomic scattering factor for X-rays. However, the atomic scattering factor for electrons is correspondingly increased since this is given by ɛ = (Z − ƒ)λ2/sin2θ, where Z is the atomic number, ƒ is the X-ray scattering factor, λ is the effective wave-length of the electron beam and θ is the Bragg angle. Hence, hydrogen ions in hydrogen bonds should be detected more readily in structure analyses based on electron diffraction data. Techniques for structure analysis using single-crystal electron diffraction patterns have been evolved and will be described elsewhere. They have been applied to the study of the structure of boric acid layers.