The crystal structure of uracil

Parry, G.

doi:10.1107/s0365110x54000904

Cited by 137 publications

(49 citation statements)

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“…The hydrogen bond N3-H3...O4 has an N3...O4 distance of 2-81/~,, an H3...O4 distance of 1.77 A and an N-H...O angle of 179.4°. * Similar dimers occur in the crystal structure of uracil itself (Parry, 1954;Stewart & Jensen, 1967) where the N3...O4 distance is 2.87 A. Note that the hydrogen bonding in the crystal structures of uracil and 1-methyluracil involves 04 as acceptor but not 02.…”

Section: Resultsmentioning

confidence: 86%

Crystal structure of 1-methyluracil from neutron diffraction at 15, 60 and 123 K

McMullan¹,

Craven²

1989

Acta Crystallogr Sect B

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Section: Resultsmentioning

confidence: 86%

Crystal structure of 1-methyluracil from neutron diffraction at 15, 60 and 123 K

McMullan¹,

Craven²

1989

Acta Crystallogr Sect B

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“…The formation of one specific crystal phase in the uracil compounds stabilized through hydrogen bonds and stacking interactions is a well-known result. 57,58 However, the inclusion of the metal ion, i.e. Na + , in a stable structure is a novel and challenging result.…”

Section: Figurementioning

confidence: 99%

Three-Dimensional Uracil Network with Sodium as a Linker

et al. 2016

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Here we show that uracil and sodium form a three-dimensional metal-mediated nucleic acid network; it is grown in atomic/molecular layer-by-layer manner using the atomic/molecular layer deposition (ALD/MLD) thin-film technique. The long-range ordered Na-uracil crystalline structure is evidenced as sharp Bragg reflections. Based on density functional theory (DFT) calculations, a tetrameric-like crystal structure is proposed. Na-uracil thin films are fluorescent with a lifetime three orders of magnitude higher than commonly seen for nucleic acid molecules. Our method provides a new approach to designing 3D nucleic acid-metal nanostructures.

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“…This is analogous to the findings that the purine base, guanine, formed almost identical structures on graphite and MoS 2 surfaces [9]. The X-ray crystal study of uracil [18] showed that the molecular packing was in the form of planar sheets parallel to the (001) surface with the uracil molecules arranged in a centrosymmetric dimer configuration. The equivalent dimensions for this arrangement (a = 1.182 nm, b = 1.235 nm and γ = 90 • ) are similar to those determined for uracil on graphite and MoS 2 .…”

Section: Scanning Tunneling Microscopymentioning

confidence: 52%

“…Similarly, the formation of these dimers into the observed herring bone pattern suggested a number of plausible configurations for the monolayer structure. This observation was pointed out by Parry in the original work on the bulk structure [18], in which two trial configurations were proposed to accommodate the space group data. The final structure was resolved by refinement of the electron density maps.…”

Section: Molecular Mechanics Simulationmentioning

confidence: 77%

Molecular mechanics simulation of uracil adlayers on molybdenum disulfide and graphite surfaces

Sowerby¹,

Edelwirth²,

Heckl³

1998

Applied Physics A: Materials Science & Processing

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Molecular mechanics using the Dreiding II force field was applied to the self-assembled monolayer configurations of the nucleic acid base uracil on molybdenum disulfide and graphite surfaces. Energy minimization calculations were used to refine the structures determined by scanning tunneling microscopy studies of the monolayer systems and allowed discrimination between competing models on the basis of final configurations and local minima convergence.The 2,4-dioxypyrimidine, uracil, has biological functions as a component of linear polymeric ribose nucleic acid (RNA). Molecular recognition between complementary subunits within these polymers is involved in the process of heredity as well as protein synthesis. The recognition processes observed in these systems involve hydrogen bond mediated complementary base pairing between uracil and the other base components within the same polymer or other polymer strands. The self-complementary interaction of uracils has been observed in nucleic acid molecules as well as in the solid state and similarly involves intermolecular hydrogen bonds [1].The formation of two-dimensional monolayers of the nucleic acid bases was first observed electrochemically on the hanging mercury drop electrode in 1965 [2, 3] although it was not until 1987 that Saffarian et al. [4] suggested that the arrangement of the molecules in these films might be oriented in a planar arrangement stabilized by self-complementary intermolecular hydrogen bonds, analogous to their arrangement in the bulk crystal. The electrochemical analysis of uracil and its derivatives is particularly detailed, and examination of these systems has provided thermodynamic and kinetic information about formation and dissolution at the mercury-water interface. Investigation of the monolayer structure, however, could only be addressed indirectly by techniques which measured thermodynamic properties, such as the interfacial tension [5,6]. The application of electrochemical scanning tunneling microscopy (ECSTM) on * Corresponding author graphite surfaces has enabled real-space investigation of the electrochemically formed monolayers [7], and similarly STM in air has been applied to monolayers on graphite [8,9] and molybdenum disulfide surfaces [9] formed by evaporation of their aqueous solutions. The ECSTM and STM studies of the nucleic acid purine and pyrimidine monolayer systems have been reviewed [10] and their spontaneous formation has been proposed to have a functional role in the origin of life [10,11].The STM study of uracil monolayers formed at the solid-liquid interface on graphite and molybdenum disulfide (MoS 2 ) surfaces has recently been performed [12]. This communication is a re-examination of those studies with the presentation of additional image data together with the application of molecular mechanics simulations.We have several reasons for performing molecular mechanics simulations on the monolayer systems of the nucleic acid bases. These include discrimination between competing structural models, providing starting...

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The crystal structure of uracil

Cited by 137 publications

References 1 publication

Crystal structure of 1-methyluracil from neutron diffraction at 15, 60 and 123 K

Crystal structure of 1-methyluracil from neutron diffraction at 15, 60 and 123 K

Three-Dimensional Uracil Network with Sodium as a Linker

Molecular mechanics simulation of uracil adlayers on molybdenum disulfide and graphite surfaces

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