The Molecular Structure of Cyclobutane

The cyclobutane molecule has been found by electron diffraction to have the following bond distances and bond angles: C–C, 1.568±0.02A; C–H, 1.098±0.04A; ∠HCH, 114±8°. On the average the ring is nonplanar, with dihedral angle 20° (+10°, −20°), but the equilibrium symmetry may be either D_(2d) (puckered ring) or D_(4h) (planar ring with low rigidity leading to large amplitude of out‐of‐plane bending). This point is discussed in connection with earlier spectroscopic work. The long bond distances found in four‐membered rings are contrasted against the short distances in three‐membered rings, and the strain energies, bond distances, and HCH angles of cycloalkanes are discussed in terms of modern valence concepts. It is suggested that the potential energy arising from a repulsion of the nonbonded carbon atoms may contribute significantly to the apparently anomalously high strain energy of cyclobutane. The repulsive force associated with such a potential is shown to account satisfactorily for the long C–C distances

The Molecular Structure of Cyclopropene, C_3C_4

Cyclopropene, C_3H_4, has been investigated by the electron diffraction method. The cyclic structure is confirmed and the following interatomic distances and angles are found: C–C, 1.525±0.02 A; C=C, 1.286±0.04 A; 〈C–H〉, 1.087±0.04 A; ∠H–C–H, 118° (assumed); ∠C=C–H, 152±12°

The Molecular Structure of Cyclobutane

The cyclobutane molecule has been found by electron diffraction to have the following bond distances and bond angles: C–C, 1.568±0.02A; C–H, 1.098±0.04A; ∠HCH, 114±8°. On the average the ring is nonplanar, with dihedral angle 20° (+10°, −20°), but the equilibrium symmetry may be either D_(2d) (puckered ring) or D_(4h) (planar ring with low rigidity leading to large amplitude of out‐of‐plane bending). This point is discussed in connection with earlier spectroscopic work. The long bond distances found in four‐membered rings are contrasted against the short distances in three‐membered rings, and the strain energies, bond distances, and HCH angles of cycloalkanes are discussed in terms of modern valence concepts. It is suggested that the potential energy arising from a repulsion of the nonbonded carbon atoms may contribute significantly to the apparently anomalously high strain energy of cyclobutane. The repulsive force associated with such a potential is shown to account satisfactorily for the long C–C distances

The Molecular Structure of Cyclopropene, C_3C_4

Cyclopropene, C_3H_4, has been investigated by the electron diffraction method. The cyclic structure is confirmed and the following interatomic distances and angles are found: C–C, 1.525±0.02 A; C=C, 1.286±0.04 A; 〈C–H〉, 1.087±0.04 A; ∠H–C–H, 118° (assumed); ∠C=C–H, 152±12°

Peak positions and shapes in neutron pair correlation functions from powders of highly anisotropic crystals

The effect of the powder average on the peak shapes and positions in neutron pair distribution functions of polycrystalline materials is examined. It is shown that for highly anisotropic crystals, the powder average leads to shifts in peak positions and to non-Gaussian peak shapes. The peak shifts can be as large as several percent of the lattice spacing

Hydration dynamics at fluorinated protein surfaces

Water-protein interactions dictate many processes crucial to protein function including folding, dynamics, interactions with other biomolecules, and enzymatic catalysis. Here we examine the effect of surface fluorination on water-protein interactions. Modification of designed coiled-coil proteins by incorporation of 5,5,5-trifluoroleucine or (4S)-2-amino-4-methylhexanoic acid enables systematic examination of the effects of side-chain volume and fluorination on solvation dynamics. Using ultrafast fluorescence spectroscopy, we find that fluorinated side chains exert electrostatic drag on neighboring water molecules, slowing water motion at the protein surface

Toward homochiral protocells in noncatalytic peptide systems

The activation-polymerization-epimerization-depolymerization (APED) model of Plasson et al. has recently been proposed as a mechanism for the evolution of homochirality on prebiotic Earth. The dynamics of the APED model in two-dimensional spatially-extended systems is investigated for various realistic reaction parameters. It is found that the APED system allows for the formation of isolated homochiral proto-domains surrounded by a racemate. A diffusive slowdown of the APED network such as induced through tidal motion or evaporating pools and lagoons leads to the stabilization of homochiral bounded structures as expected in the first self-assembled protocells.Comment: 10 pages, 5 figure

Chiral Polymerization in Open Systems From Chiral-Selective Reaction Rates

We investigate the possibility that prebiotic homochirality can be achieved exclusively through chiral-selective reaction rate parameters without any other explicit mechanism for chiral bias. Specifically, we examine an open network of polymerization reactions, where the reaction rates can have chiral-selective values. The reactions are neither autocatalytic nor do they contain explicit enantiomeric cross-inhibition terms. We are thus investigating how rare a set of chiral-selective reaction rates needs to be in order to generate a reasonable amount of chiral bias. We quantify our results adopting a statistical approach: varying both the mean value and the rms dispersion of the relevant reaction rates, we show that moderate to high levels of chiral excess can be achieved with fairly small chiral bias, below 10%. Considering the various unknowns related to prebiotic chemical networks in early Earth and the dependence of reaction rates to environmental properties such as temperature and pressure variations, we argue that homochirality could have been achieved from moderate amounts of chiral selectivity in the reaction rates.Comment: 15 pages, 6 figures, accepted for publication in Origins of Life and Evolution of Biosphere

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Position-dependent effects on stability in tricyclo-DNA modified oligonucleotide duplexes

A series of oligodeoxyribonucleotides and oligoribonucleotides containing single and multiple tricyclo(tc)-nucleosides in various arrangements were prepared and the thermal and thermodynamic transition profiles of duplexes with complementary DNA and RNA evaluated. Tc-residues aligned in a non-continuous fashion in an RNA strand significantly decrease affinity to complementary RNA and DNA, mostly as a consequence of a loss of pairing enthalpy ΔH. Arranging the tc-residues in a continuous fashion rescues Tm and leads to higher DNA and RNA affinity. Substitution of oligodeoxyribonucleotides in the same way causes much less differences in Tm when paired to complementary DNA and leads to substantial increases in Tm when paired to complementary RNA. CD-spectroscopic investigations in combination with molecular dynamics simulations of duplexes with single modifications show that tc-residues in the RNA backbone distinctly influence the conformation of the neighboring nucleotides forcing them into higher energy conformations, while tc-residues in the DNA backbone seem to have negligible influence on the nearest neighbor conformations. These results rationalize the observed affinity differences and are of relevance for the design of tc-DNA containing oligonucleotides for applications in antisense or RNAi therapy