Crystal structure of a naturally occurring dinucleoside monophosphate: uridylyl (3',5') adenosine hemihydrate

The crystal structure of uridylyl (3',5') adenosine hemihydrate has been analyzed by x-ray diffraction. The two independent molecules found in the asymmetric unit exhibit conformations that differ significantly from those found in double-helical RNA. The conformational information obtained from this analysis provides considerable insight into the possible conformations of nonhelical "loop" regions of transfer RNA, as well as single-stranded regions of nucleic acids in general.     

Crystal structure of the 1: 1 complex of 5-fluorouracil and 9-ethylhypoxanthine

9-Ethylhypoxanthine and 5-fluorouracil form a 1 : 1 crystalline complex. The structure of this complex has been solved by x-ray diffraction analysis. The molecules crystallize in a monoclinic lattice and form a sheet structure in which pairs of fluorouracil molecules are held together by two hydrogen bonds. The 9-ethylhypoxanthine residues fill up the rest of the molecular sheet by forming single hydrogen bonds with each uracil pair.     

The anticodon contains a major element of the identity of arginine transfer RNAs

The contribution of the anticodon to the discrimination between cognate and noncognate tRNAs by Escherichia coli Arg-tRNA synthetase has been investigated by in vitro synthesis and aminoacylation of elongator methionine tRNA (tRNA(mMet) mutants. Substitution of the Arg anticodon CCG for the Met anticodon CAU leads to a dramatic increase in Arg acceptance by tRNA(mMet). A nucleotide (A20) previously identified by others in the dihydrouridine loop of tRNA(Arg)s makes a smaller contribution to the conversion of tRNA(mMet) identity from Met to Arg. The combined anticodon and dihydrouridine loop mutations yield a tRNA(mMet) derivative that is aminoacylated with near-normal kinetics by the Arg-tRNA synthetase.     

Formation of a one-dimensional array of oxygen in a microporous metal-organic solid

We report the direct observation of dioxygen molecules physisorbed in the nanochannels of a microporous copper coordination polymer by the MEM (maximum entropy method)/Rietveld method, using in situ high-resolution synchrotron x-ray powder diffraction measurements. The obtained MEM electron density revealed that van der Waals dimers of physisorbed O2 locate in the middle of nanochannels and form a one-dimensional ladder structure aligned to the host channel structure. The observed O-O stretching Raman band and magnetic susceptibilities are characteristic of the confined O2 molecules in one-dimensional nanochannels of CPL-1 (coordination polymer 1 with pillared layer structure).     

The structure of the first coordination shell in liquid water

X-ray absorption spectroscopy and x-ray Raman scattering were used to probe the molecular arrangement in the first coordination shell of liquid water. The local structure is characterized by comparison with bulk and surface of ordinary hexagonal ice Ih and with calculated spectra. Most molecules in liquid water are in two hydrogen-bonded configurations with one strong donor and one strong acceptor hydrogen bond in contrast to the four hydrogen-bonded tetrahedral structure in ice. Upon heating from 25 degrees C to 90 degrees C, 5 to 10% of the molecules change from tetrahedral environments to two hydrogen-bonded configurations. Our findings are consistent with neutron and x-ray diffraction data, and combining the results sets a strong limit for possible local structure distributions in liquid water. Serious discrepancies with structures based on current molecular dynamics simulations are observed.     

Crystal and molecular structure of adenosine 3',5'-cyclic phosphate

The structure of adenosine 3',5'-cyclic phosphate has been determined by single-crystal x-ray diffraction. The two molecules in the asymmetric unit show different conformation about the glycosidic bond, while other structural details are essentially the same. The furanose rings are puckered with the C(4') atom out of the best four-atom plane. The bond lengths and angles appear to be normal.     

Crystal Structures at High Pressures of Metallic Modifications of Silicon and Germanium

Studies of germanium and silicon by x-ray diffraction reveal that their crystal structure changes at high pressures from the semiconducting diamond-type structure to the metallic white tin structure, in analogy to the known "gray" to "white" transition in tin itself.     

Smectic liquid crystal monolayers on graphite observed by scanning tunneling microscopy

By means of scanning tunneling microscopy, it is observed that molecules of the form n-alkylcyanobiphenyl, where n = 8 to 12, form two-dimensional crystalline domains when adsorbed onto graphite. The layer spacings measured by tunneling microscopy are 20% larger than those measured previously on bulk material by x-ray diffraction. The structure of the adsorbed molecules is quite different from that of the bulk.     

Solution of a protein crystal structure with a model obtained from NMR interproton distance restraints

Model calculations were performed to test the possibility of solving crystal structures of proteins by Patterson search techniques with three-dimensional structures obtained from nuclear magnetic resonance (NMR) interproton distance restraints. Structures for crambin obtained from simulated NMR data were used as the test system; the root-mean-square deviations of the NMR structures from the x-ray structure were 1.5 to 2.2 A for backbone atoms and 2.0 to 2.8 A for side-chain atoms. Patterson searches were made to determine the orientation and position of the NMR structures in the unit cell. The correct solution was obtained by comparing the rotation function results of several of the NMR structures and the average structure derived from them. Conventional refinement techniques reduced the R factor from 0.43 at 4 A resolution to 0.27 at 2 A resolution without inclusion of water molecules. The partially refined structure has root-mean-square backbone and side-chain atom deviations from the x-ray structure of 0.5 and 1.3 A, respectively.     

Structure of langmuir-blodgett films of disk-shaped molecules determined by atomic force microscopy

Monolayer Langmuir-Blodgett films of a discotic mesogen have been studied with atomic force microscopy (AFM). These measurements confirm the "edge on" arrangement for the disk-shaped molecules suggested by surface pressure-area isotherms and show that the molecules form columns that are separated by 17.7 angstroms +/- 10 percent. Column alignment is found to be predominantly along the film deposition direction, with an angular spread of 35 degrees . The AFM images also show that the mean disk separation within the columns is 5.1 +/- 1.3 angstroms, in good agreement with x-ray diffraction (XRD) results. Roomtemperature XRD measurements on bulk samples of the same material indicate a disordered-hexagonal liquid crystalline mesophase, with a column-to-column spacing of 19.9 +/- 0.2 angstroms.     

Molybdenum disulfide in the poorly crystalline "rag" structure

Molybdenum disulfide has been prepared in an unusual poorly crystalline form, termed the "rag" structure, consisting of several stacked but highly folded and disordered S-Mo-S layers. This previously unknown structure demonstrates the flexible and macromolecular nature of the layered transition metal dichalcogenides. The determination of this structure provides a basis for understanding its highly broadened x-ray diffraction pattern and relatively low surface area, and is a starting point for optimizing the catalytic and surface properties of molybdenum disulfide.     

The structure of the c60 molecule: x-ray crystal structure determination of a twin at 110 k

Single-crystal x-ray diffraction methods were used to determine the crystal and molecular structure of C(60) buckminsterfullerene. At 110 kelvin C(60) is cubic, apparent Laue symmetry m3m, but it exhibits noncrystallographic systematic extinctions indicative of a twin in which I(hkl) and I(khl) are superimposed. In fact, C(60) crystallizes with four molecules in space group [See equation in the PDF file] of the cubic system (Laue symmetry m3) with lattice constant a = 14.052(5) angstroms (A) at 110 kelvin. The twin components are equal. A given component, which has crystallographically imposed symmetry [See equation in the PDF file] displays an ordered structure of a truncated icosahedron. The five independent C=C bonds that join C(6) rings average 1.355(9) A; the ten independent C-C bonds that join C(6) and C(5) rings average 1.467(21) A. The mean atom-to-atom diameter of the C(60) molecule is 7.065(3) A. The molecules are very tightly packed in the crystal structure, with intermolecular C...C distances as short as 3.131(7) A.     

Topochemical polymerization of C70 controlled by monomer crystal packing

Polymeric forms of C60 are now well known, but numerous attempts to obtain C70 in a polymeric state have yielded only dimers. Polymeric C70 has now been synthesized by treatment of hexagonally packed C70 single crystals under moderate hydrostatic pressure (2 gigapascals) at elevated temperature (300 degrees C), which confirms predictions from our modeling of polymeric structures of C70. Single-crystal x-ray diffraction shows that the molecules are bridged into polymeric zigzag chains that extend along the c axis of the parent structure. Solid-state nuclear magnetic resonance and Raman data provide evidence for covalent chemical bonding between the C70 cages.     

High-resolution protein structure determination by serial femtosecond crystallography

Structure determination of proteins and other macromolecules has historically required the growth of high-quality crystals sufficiently large to diffract x-rays efficiently while withstanding radiation damage. We applied serial femtosecond crystallography (SFX) using an x-ray free-electron laser (XFEL) to obtain high-resolution structural information from microcrystals (less than 1 micrometer by 1 micrometer by 3 micrometers) of the well-characterized model protein lysozyme. The agreement with synchrotron data demonstrates the immediate relevance of SFX for analyzing the structure of the large group of difficult-to-crystallize molecules.     

Imidodiphosphate and pyrophosphate: possible biological significance of similar structures

The structure of sodium imidodiphosphate has been determined by single crystal x-ray diffraction. The P-N-P bond angle (127.2 degrees) and P-N bond distance (1.68 angstroms) are remarkably similar to newly refined values for the P-O-P bond angle (128.6 degrees) and the bridging P-O bond distance (1.63 angstroms) of sodium pyrophosphate. This close similarity may explain why P-N-P linkages in algal "polyphosphates" escaped detection until recently and why adenosine triphosphate analogs with this linkage mimic adenosine triphosphate so closely.     

X-ray diffraction and computation yield the structure of alkanethiols on gold(111)

The structure of self-assembled monolayers (SAMs) of long-chain alkyl sulfides on gold(111) has been resolved by density functional theory-based molecular dynamics simulations and grazing incidence x-ray diffraction for hexanethiol and methylthiol. The analysis of molecular dynamics trajectories and the relative energies of possible SAM structures suggest a competition between SAM ordering, driven by the lateral van der Waals interaction between alkyl chains, and disordering of interfacial Au atoms, driven by the sulfur-gold interaction. We found that the sulfur atoms of the molecules bind at two distinct surface sites, and that the first gold surface layer contains gold atom vacancies (which are partially redistributed over different sites) as well as gold adatoms that are laterally bound to two sulfur atoms.     

Electron- and photon-stimulated desorption: probes of structure and bonding at surfaces

Techniques for analyzing the structure and composition of solid surfaces with electron and photon beams often cause radiation damage in samples. Damage-producing processes compete with information-producing events during measurements, and beam damage can be a serious perturbation in quantitative surface analysis. There are, however, substantial benefits of electron- and photonstimulated damage processes for studying molecules adsorbed on surfaces. Direct information about the geometric structure of surface molecules can be obtained from measurements of the angular distributions of ions released by electron- or photon-stimulated desorption. The directions of ion emission are determined by the orientation of the surface bonds that are ruptured by beam irradiation. Moreover, photon-stimulated desorption studies that make use of synchrotron radiation reveal the fundamental electronic excitations that lead to bondbreaking processes at surfaces. These measurements provide new insights into radiation-damage processes in areas as diverse as x-ray optics and semiconductor electronics.     

Structure of haloform intercalated C60 and its influence on superconductive properties

CHCl3 and CHBr3 intercalated C60 have attracted particular interest after a superconductivity transition temperature (Tc) of up to 117 K was discovered. We have determined the structure using synchrotron x-ray powder-diffraction and found that the expansion of the lattice mainly takes place in one dimension (triclinic b axis), leaving planes of C60 molecules on an approximately hexagonal, slightly expanded lattice. We have performed tight-binding band structure calculations for the surface layer. In spite of the slight expansion of the layers, for the range of dopings where a large Tc has been observed, the density of states at the Fermi energy is smaller for C60.2CHCl3 and C60.2CHBr3 than for C60. This suggests that the lattice expansion alone cannot explain the increase of Tc.     

Structure of the multidrug transporter EmrD from Escherichia coli

EmrD is a multidrug transporter from the Major Facilitator Superfamily that expels amphipathic compounds across the inner membrane of Escherichia coli. Here, we report the x-ray structure of EmrD determined to a resolution of 3.5 angstroms. The structure reveals an interior that is composed mostly of hydrophobic residues, which is consistent with its role transporting amphipathic molecules. Two long loops extend into the inner leaflet side of the cell membrane. This region can serve to recognize and bind substrate directly from the lipid bilayer. We propose that multisubstrate specificity, binding, and transport are facilitated by these loop regions and the internal cavity.