Single-Crystal X-ray Diffraction Structure of the Stable Enol Tautomer Polymorph of Barbituric Acid at 224 and 95†K.

The thermodynamically stable enol crystal form of barbituric acid, previously prepared as powder by grinding or slurry methods, has been obtained as single crystals by slow cooling from methanol solution. The selection of the enol crystal was facilitated by a density-gradient method. The structure at 224 and 95 K confirms the enol inferred on the basis of powder data. The enol has bond lengths that are consistent with the expected bond order and with DFT calculations that include treatment of hydrogen bonding. In isolation, the enol is higher in energy than the tri-keto form by 50 kJ mol(-1) which must be more than compensated by enhanced hydrogen bonding. Both crystal forms have four normal H-bonds; the enol has two additional H-bonds with O-O distances of 2.49 Å. Conversion into the enol form occurs spontaneously in the solid state upon prolonged storage of the commercial tri-keto material. Slurry conversion of tri-one to enol in ethanol is reversed in direction in ethanol-D1.

Zero-point corrections for isotropic coupling constants for cyclohexadienyl radical, C6H7 and C6H6Mu: beyond the bond length change approximation.

Zero-point vibrational level averaging for electron spin resonance (ESR) and muon spin resonance (µSR) hyperfine coupling constants (HFCCs) are computed for H and Mu isotopomers of the cyclohexadienyl radical. A local mode approximation previously developed for computation of the effect of replacement of H by D on ¹³C-NMR chemical shifts is used. DFT methods are used to compute the change in energy and HFCCs when the geometry is changed from the equilibrium values for the stretch and both bend degrees of freedom. This variation is then averaged over the probability distribution for each degree of freedom. The method is tested using data for the methylene group of C6H7, cyclohexadienyl radical and its Mu analog. Good agreement is found for the difference between the HFCCs for Mu and H of CHMu and that for H of CHMu and CH2 of the parent radical methylene group. All three of these HFCCs are the same in the absence of the zero point average, a one-parameter fit of the static HFCC, a(0), can be computed. That value, 45.2 Gauss, is compared to the results of several fixed geometry electronic structure computations. The HFCC values for the ortho, meta and para H atoms are then discussed.

Effects of the nature and concentration of salt on the interaction of the HIV-1 nucleocapsid protein with SL3 RNA.

The mature nucleocapsid protein of HIV-1, NCp7, and the NC domains in gag precursors are attractive targets for anti-AIDS drug discovery. The stability of the 1:1 complex of NCp7 with a 20mer mimic of stem-loop 3 RNA (SL3, also called psi-RNA, in the packaging domain of genomic RNA) is strongly affected by changes in ionic strength. NC domains recognize and specifically package genomic HIV-1 RNA, while electrostatic attractions and high concentrations of protein and RNA drive NCp7 to completely coat the RNA in the mature virion. The specific interactions of NCp7 binding to loop bases of SL3 produce 1:1 complexes in solutions that have a NaCl concentration of >or=0.2 M, while the electrostatic interactions can dominate at

The vibrational spectrum of parabanic acid by inelastic neutron scattering spectroscopy and simulation by solid-state DFT.

The incoherent inelastic neutron scattering spectrum of parabanic acid was measured and simulated using solid-state density functional theory (DFT). This molecule was previously the subject of low-temperature X-ray and neutron diffraction studies. While the simulated spectra from several density functionals account for relative intensities and factor group splitting regardless of functional choice, the hydrogen-bending vibrational energies for the out-of-plane modes are poorly described by all methods. The disagreement between calculated and observed out-of-plane hydrogen bending mode energies is examined along with geometry optimization differences of bond lengths, bond angles, and hydrogen-bonding interactions for different functionals. Neutron diffraction suggests nearly symmetric hydrogen atom positions in the crystalline solid for both heavy-atom and N-H bond distances but different hydrogen-bonding angles. The spectroscopic results suggest a significant factor group splitting for the out-of-plane bending motions associated with the hydrogen atoms (N-H) for both the symmetric and asymmetric bending modes, as is also supported by DFT simulations. The differences between the quality of the crystallographic and spectroscopic simulations by isolated-molecule DFT, cluster-based DFT (that account for only the hydrogen-bonding interactions around a single molecule), and solid-state DFT are considered in detail, with parabanic acid serving as an excellent case study due to its small size and the availability of high-quality structure data. These calculations show that hydrogen bonding results in a change in the bond distances and bond angles of parabanic acid from the free molecule values.

Inelastic neutron scattering and Raman spectroscopic investigation of L-alanine alaninium nitrate, a homologue of a ferroelectric material.

The 2 : 1 amino acid salt of L-alanine with nitric acid was crystallized and the vibrational spectrum measured at 25 K by incoherent inelastic neutron scattering (INS) spectroscopy. The spectrum was simulated using solid-state density functional theory based on a new 90 K structure determination. A feature observed at approximately 450 cm(-1) in the INS spectrum of L-alanine alaninium nitrate is noticeably absent in the calculation. Raman spectroscopy reveals spectral differences between the spectra at 77 and 293 K with a 450 cm(-1) feature appearing at low temperature. The nature of these spectral changes and the disagreement between the INS spectrum and its simulation are discussed in relation to an apparent structural change involving motion of a proton at low (<90 K) temperature.

Vicinal deuterium perturbations on hydrogen NMR chemical shifts in cyclohexanes.

The substitution of a deuterium for a hydrogen is known to perturb the NMR chemical shift of a neighboring hydrogen atom. The magnitude of such a perturbation may depend on the specifics of bonding and stereochemical relationships within a molecule. For deuterium-labeled cyclohexanes held in a chair conformation at -80 degrees C or lower, all four possible perturbations of H by D as H-C-C-H is changed to D-C-C-H have been determined experimentally, and the variations seen, ranging from 6.9 to 10.4 ppb, have been calculated from theory and computational methods. The predominant physical origins of the NMR chemical shift perturbations in deuterium-labeled cyclohexanes have been identified and quantified. The trends defined by the Delta delta perturbation values obtained through spectroscopic experiments and by theory agree satisfactorily. They do not match the variations typically observed in vicinal J(H-H) coupling constants as a function of dihedral angles.

Polyacetylene: Myth and Reality.

Polyacetylene, the simplest and oldest of potentially conducting polymers, has never been made in a form that permits rigorous determination of its structure. Trans polyacetylene in its fully extended form will have a potential energy surface with two equivalent minima. It has been assumed that this results in bond length alternation. It is, rather, very likely that the zero-point energy is above the Peierls barrier. The experimental studies that purport to show bond alternation are reviewed and shown to be compromised by serious experimental inconsistencies or by the presence, for which there is considerable evidence, of finite chain polyenes. In this view, addition of dopants results in conductivity by facilitation of charge transport between finite polyenes. The double minimum potential that necessarily occurs for polyacetylene, if viewed as the result of elongation of finite chains, originates from admixture of the 1¹Ag ground electronic state with the 2¹Ag excited electronic singlet state. This excitation is diradical (two electron) in character. The polyacetylene limit is an equal admixture of these two ¹Ag states making theory intractable for long chains. A method is outlined for preparation of high molecular weight polyacetylene with fully extended chains that are prevented from reacting with neighboring chains.

Hydrothermal and structural chemistry of the zinc(II)- and cadmium(II)-1,2,4-triazolate systems.

Hydrothermal reactions of 1,2,4-triazole with zinc and cadmium salts have yielded 10 structurally unique materials of the M(II)/trz/Xn- system, with M(II)=Zn and Cd and Xn-=F-, Cl-, Br-, I-, OH-, NO3-, and SO(4)2- (trz=1,2,4-triazolate). Of the zinc-containing phases, [Zn(trz)2] (1), [Zn2(trz)3(OH)].3H2O (3.3H2O), and [Zn2(trz)(SO4)(OH)] (4) are three-dimensional, while [Zn(trz)Br] (2) is two-dimensional. All six cadmium phases, [Cd3(trz)3F2(H2O)].2.75H2O (5.2.75H2O), [Cd2(trz)2Cl2(H2O)] (6), [Cd3(trz)3Br3] (7), [Cd2(trz)3I] (8), [Cd3(trz)5(NO3)(H2O)].H2O (9.H2O), and [Cd8(trz)4(OH)2(SO4)5(H2O)] (10), are three-dimensional. In all cases, the anionic components Xn- participate in the framework connectivity as bridging ligands. The structural diversity of these materials is reflected in the variety of coordination polyhedra displayed by the metal sites: tetrahedral; trigonal bipyramidal; octahedral. Structures 3, 5, and 7-9 exhibit two distinct polyhedral building blocks. The materials are also characterized by a range of substructural components, including trinuclear and tetranuclear clusters, adamantoid cages, chains, layers, and complex frameworks.

A nucleic acid switch triggered by the HIV-1 nucleocapsid protein.

A unimolecular oligonucleotide switch, termed here an AlloSwitch, binds the mature HIV-1 nucleocapsid protein, NCp7. This switch can be used as an indicator for the presence of free NCp7 and NC domains in precursor and fusion proteins. It is thermodynamically stable in two conformations, H and O. A FRET pair is covalently attached to the strands to report on the molecular state of the switch. The results show that NC has an affinity for O 170 times higher than its affinity for H and that in the absence of NC the equilibrium ratio K1 = [O]/[H] = 0.10 +/- 0.03 for the switch sequence reported here. The change between the two states happens on a rapid kinetic time scale. A framework is introduced to aid in the design of AlloSwitches aimed at other targets. A high-affinity probe segment must be available to bind the target in the O-form, while a cover segment hides the probe in H. A key is adjusting the cover sequence to favor the H-form by a factor of 10-1000. This affords a robust response to small changes in target concentration, while saturation produces more than 90% of the maximal change in fluorescence. When a competitor displaces the switch from the NC-O complex, the released switch reverts to the H-form. This is the basis for a mix-and-read strategy for high-throughput screening of anti-nucleocapsid drug candidates that is much simpler to execute than traditional assays that require immobilization and washing steps.

Rapid exchange luminescence: nitroxide quenching and implications for sensor applications.

The quenching of terbium emission in the sensitized complex Tb3+-cs124-DTPA by nitroxide radical TEMPO derivatives in aqueous solutions has been studied with time-averaged and time-resolved methods. The time-resolved results show more quenching than the time-averaged values, opposite to the behavior expected for static quenching. A rapid exchange model with a slightly fluorescent fluorophore/quencher complex is proposed. Due to the long time scale of Tb3+ emission, dynamical averaging must be considered in the interpretation of experiments. The rapid exchange limit is shown to be consistent with the present results. The utility of these observations in the design of sensors that are not limited by a background level is noted.

Inelastic neutron scattering spectrum of Cs2[B12H12]: reproduction of its solid-state vibrational spectrum by periodic DFT.

The inelastic neutron scattering (INS) spectrum of polycrystalline Cs2[B12H12] is assigned through 1200 cm(-1) on the basis of aqueous and solid-state Raman/IR measurements and normal mode analyses from solid-state density functional theory. The Cs+ cations are responsible for frequency shifts of the internal cage vibrational modes and I(h) cage mode splittings due to the crystal T(h) site symmetry. These changes to the [B12H12]2- molecular modes make isolated-molecule calculations inadequate for use in complete assignments. Solid-state calculations reveal that 30/40 cm(-1) shifts of Tg/Hg molecular modes are responsible for structure in the INS spectrum unobserved by optical methods or in aqueous solutions.

Conformational distinguishability of medium cycloalkanes in crystals via inelastic neutron scattering.

This paper begins an exploration of the use of the combination of DFT computations with experimental inelastic neutron scattering (INS) spectra as a method for establishing what conformation is present in a molecular crystal at low temperature. Presented here are INS spectra of a series of medium-sized cycloalkanes: C6H12, C7H14, C8H16, C10H20, C12H24, and C14H28. Optimized geometries and normal mode calculations were performed at B3LYP/6-311G(d,p) on the lowest energy conformations (i.e., those thermally accessible at the experimental temperature of 30 K). The calculated and observed spectra were analyzed for the best fit from each set of conformers, allowing a prediction of the dominant conformation in a conformationally rich system. For each cycloalkane, the calculated spectrum for the lowest energy conformer shows good agreement with experiment while the higher energy conformations have a much poorer fit. With little ambiguity, the lowest energy conformer is therefore predicted to be the dominant conformation, consistent with the diffraction data available for C6H12, C10H20, C12H24, and C14H28. These results indicate that INS spectroscopy may be a useful tool in determining the dominant conformation in a crystal lattice in cases such as this in which the intermolecular interactions are weak and the different conformers are calculated to have distinguishable spectra. Such an analysis is applied to the cases of C7H14 and C8H16 for which no low-temperature X-ray analysis is available. Clear structure predictions result, and the conformer observed is that computed to be of lowest energy for the molecule in isolation.

Spectroscopic and ab initio characterization of the [ReH9]2- ion.

The dynamics and bonding of the hydrido complex Ba[ReH9], containing the D3h face-capped trigonal prismatic [ReH9]2- ion, have been investigated by vibrational spectroscopy and density functional theory (DFT). The combination of infrared, Raman, and inelastic neutron-scattering (INS) spectroscopies has enabled observation of all the modes of the [ReH9]2- ion for the first time. We demonstrate that calculations of the isolated [ReH9]2- ion are unable to reproduce the INS spectrum and that the complete unit cell must be considered with periodic DFT to have reliable results. This is shown to be a consequence of the long-range Coulomb potential present. Analysis of the electronic structure shows that the bonding between the rhenium and the hydrogen is largely covalent. There is a small degree of covalency between the prism hydrides and the barium. The counterion is crucial to the stability of the materials; hence, variation of it potentially offers a method to fine-tune the properties of the material.

Inelastic neutron scattering spectra of free base and zinc porphines: a comparison with DFT-based vibrational analysis.

Inelastic neutron scattering (INS) spectra of free base (FBP) and zinc (ZnP) porphines are presented and compared with the results of density functional theory (DFT) calculations using the B3LYP functional with 6-31G(d) or 6-311G(d,p) basis sets. To obtain quantitative agreement between experiment and theory, two different scaling techniques have been applied: a scaled quantum mechanical (DFT-SQM) force field was developed for B3LYP/6-31G(d) calculations and the uniform frequency scaling technique (DFT-UFS) was applied to B3LYP/6-311G(d,p) results. The DFT-SQM calculations have been previously compared with IR and Raman spectra with good agreement, which allows for a nearly complete vibrational assignment. The results of the present study extend previous vibrational analysis to a higher level of reliability and complexity. The previous results are augmented by the comparison of calculated and observed INS intensities and the comparison of calculated modes with those observed in INS spectra but previously unobserved in optical spectra. Excellent agreement is acquired between the INS spectra and the results of both calculations, permitting a more detailed and reliable description of the vibrational properties of porphyrins.

Infrared, Raman, and inelastic neutron scattering spectra of dodecahedrane: an I(h) molecule in T(h) site symmetry.

The Raman spectrum of crystalline dodecahedrane, C20H20, a species of nominal I(h) symmetry, exhibits splitting of the H(g) Raman active modes. The Raman inactive gerade vibrations of G(g), T(1g), and T(2g) symmetry are found to have weak Raman activity. The IR forbidden vibrations of T(2u), G(u), and H(u) type have moderate IR activity. All of this is consistent with the T(h) site symmetry. A treatment of the structure and vibrations of dodecahedrane using a periodic lattice DFT method results in a slightly distorted T(h) structure with six C-C bonds that are 0.001 A longer than the other 24. The vibrational spectrum computed for this structure exhibits splittings of the H(g) modes that are consistent with the observed spectra, but the computed splittings are larger than observed in room-temperature data. A complex pattern observed in the C-H stretching region is assigned. The inelastic neutron scattering spectrum calculated from the computed normal modes for the T(h) molecule in the lattice agrees quantitatively with experiment when overtone and combination transitions are included and allowance is made for anharmonicity of the C-H stretch motion. Finally, it is argued that the existing crystallographic determination of the average C-C bond length of 1.544 A is shortened by disorder and should be revised upward to agree with the computed value of 1.558 A.

The inelastic neutron scattering spectrum of H3B:NH3 and the reproduction of its solid-state features by periodic DFT.

The inelastic neutron scattering (INS) and periodic density functional theory (DFT) vibrational spectra of H3B:NH3 are reported to 1600 cm-1. The H3B:NH3 structural and INS features, specifically the reduced solid-state B:N dative bond length and the altered B:N stretching frequency, are reproduced by the periodic DFT calculations, placing the B:N stretching mode at 800 cm-1, in excellent agreement with experiment relative to previous nonperiodic theoretical treatments of this molecule.

Affinities of the nucleocapsid protein for variants of SL3 RNA in HIV-1.

Efficient packaging of genomic RNA into new HIV-1 virus particles requires that nucleocapsid domains of precursor proteins bind the SL3 tetraloop (G317-G-A-G320) from the 5'-untranslated region. This paper presents the affinities of 35 RNA variants of SL3 for the mature 55mer NC protein, as measured by fluorescence quenching of tryptophan-37 in the protein by nucleobases. The 1:1 complexes that form in 0.2 M NaCl have dissociation constants ranging from 8 nM (GGUG) to 20 microM (GAUA). The highly conserved (GGAG) sequence for the wild type is not the most stable (K(d) = 28 nM), suggesting that other selective pressures beyond the stability of the complex must be satisfied. The leading requirement for strong interaction is for G320, followed closely by G318. Replacing either with U, A, or C reduces affinity by a factor of 15-120. NC-domains from multiple proteins combine to recognize unpaired G(2)-loci, where two guanines are in close proximity. We have previously measured affinities of the NC protein for the important stem-loops of the major packaging domain [Shubsda, M. F., Paoletti, A. C., Hudson, B. S., and Borer, P. N. (2002) Biochemistry 41, 5276-82]. Comparison with the present work shows that the nature of the stem also modulates NC-RNA interactions. Placing the G(2)-loci from the apical SL2 or SL1 loops on the SL3 stem increases affinity by a factor of 2-3, while placing the SL4 loop on the SL3 stem reduces affinity 50-fold. These results are interesting in the context of RNA-protein interaction, as well as for the discovery of antiNC agents for AIDS therapy.

An examination of metal-ligand binding modes in rubidium diphenylmethanide.

A powerful new synthetic method allows for the exploration of an interesting class of rubidium diphenylmethanides showing different solid-state modifications depending on the crystallization temperatures. Theoretical and structural analysis in the solution and the solid state leads to a broader understanding of metal-ligand binding modes.

Affinities of packaging domain loops in HIV-1 RNA for the nucleocapsid protein.

To design anti-nucleocapsid drugs, it is useful to know the affinities the protein has for its natural substrates under physiological conditions. Dissociation equilibrium constants are reported for seven RNA stem-loops bound to the mature HIV-1 nucleocapsid protein, NCp7. The loops include SL1, SL2, SL3, and SL4 from the major packaging domain of genomic RNA. The binding assay is based on quenching the fluorescence of tryptophan-37 in the protein by G residues in the single-stranded loops. Tightly bound RNA molecules quench nearly all the fluorescence of freshly purified NCp7 in 0.2 M NaCl. In contrast, when the GGAG-tetraloop of tight-binding SL3 is replaced with UUCG or GAUA, quenching is almost nil, indicating very low affinity. Interpreting fluorescence titrations in terms of a rapidly equilibrating 1:1 complex explains nearly all of the experimental variance for the loops. Analyzed in this way, the highest affinities are for 20mer SL3 and 19mer SL2 hairpin constructs (K(d) = 28 +/- 3 and 23 +/- 2 nM, respectively). The 20mer stem-UUCG-loop and GAUA-loop constructs have <0.5% of the affinity for NCp7 relative to SL3. Affinities relative to SL3 for the other stem-loops are the following: 10% for a 16mer construct to model SL4, 30% for a 27mer model of the 9-residue apical loop of SL1, and 20% for a 23mer model of a 1 x 3 asymmetric internal loop in SL1. A 154mer construct that includes all four stem-loops binds tightly to NCp7, with the equivalent of three NCp7 molecules bound with high affinity per RNA; it is also possible that two strong sites and several weaker ones combine to give the appearance of three strong sites.