Showing papers on "Dihedral angle published in 1998"

DNA bending: The prevalence of kinkiness and the virtues of normality

Abstract: DNA bending in 86 complexes with sequence-specific proteins has been examined using normal vector plots, matrices of normal vector angles between all base pairs in the helix, and one-digit roll/slide/twist tables. FREEHELIX, a new program especially designed to analyze severely bent and kinked duplexes, generates the foregoing quantities plus local roll, tilt, twist, slide, shift and rise parameters that are completely free of any assumptions about an overall helix axis. In nearly every case, bending results from positive roll at pyrimidine-purine base pair steps: C-A (= T-G), T-A, or less frequently C-G, in a direction that compresses the major groove. Normal vector plots reveal three well-defined types of bending among the 86 examples: (i) localized kinks produced by positive roll at one or two discrete base pairs steps, (ii) three-dimensional writhe resulting from positive roll at a series of adjacent base pairs steps, or (iii) continuous curvature produced by alternations of positive and negative roll every 5 bp, with side-to-side zig-zag roll at intermediate position. In no case is tilt a significant component of the bending process. In sequences with two localized kinks, such as CAP and IHF, the dihedral angle formed by the three helix segments is a linear function of the number of base pair steps between kinks: dihedral angle = 36 degrees x kink separation. Twenty-eight of the 86 examples can be described as major bends, and significant elements in the recognition of a given base sequence by protein. But even the minor bends play a role in fine-tuning protein/DNA interactions. Sequence-dependent helix deformability is an important component of protein/DNA recognition, alongside the more generally recognized patterns of hydrogen bonding. The combination of FREEHELIX, normal vector plots, full vector angle matrices, and one-digit roll/slide/twist tables affords a rapid and convenient method for assessing bending in DNA.

A statistical mechanical model for β-hairpin kinetics

Abstract: Understanding the mechanism of protein secondary structure formation is an essential part of the protein-folding puzzle. Here, we describe a simple statistical mechanical model for the formation of a β-hairpin, the minimal structural element of the antiparallel β-pleated sheet. The model accurately describes the thermodynamic and kinetic behavior of a 16-residue, β-hairpin-forming peptide, successfully explaining its two-state behavior and apparent negative activation energy for folding. The model classifies structures according to their backbone conformation, defined by 15 pairs of dihedral angles, and is further simplified by considering only the 120 structures with contiguous stretches of native pairs of backbone dihedral angles. This single sequence approximation is tested by comparison with a more complete model that includes the 215 possible conformations and 15 × 215 possible kinetic transitions. Finally, we use the model to predict the equilibrium unfolding curves and kinetics for several variants of the β-hairpin peptide.

Product rotational polarization in the photoinitiated bimolecular reaction A+BC→AB+C on attractive, mixed and repulsive surfaces

Abstract: The product rotational polarization is reported using the quasiclassical trajectory method for the photoinitiated bimolecular reaction A+BC→AB+C. The model takes the form of a 3D quasiclassical trajectory study of a hypothetical exothermic reaction employing combinations of (a): three different potential energy surfaces (attractive, mixed and repulsive), (b): three markedly different reagent mass combinations (H+HL, H+LL and H+HH, where L≡1 amu and H≡80 amu). Four PDDCSs (2π/σ) (dσ00/dωt), (2π/σ) (dσ20/dωt), (2π/σ) (dσ22+/dωt), and (2π/σ) (dσ21−/dωt) which are usually sensitive to many photoinitiated bimolecular reaction experiments are presented. Furthermore, the distribution of dihedral angle P(φr) and the distribution of angle between K and J′ P(θr) are discussed. Moreover, the angular distribution of product rotational vectors in the form of polar plots in θr and φr is calculated.

Product rotational polarization in photo-initiated bimolecular reactions A+BC: Dependence on the character of the potential energy surface for different mass combinations

Abstract: In cases of light-heavy-light (LHL), light-light-heavy (LLH), and light-heavy-heavy (LHH) mass combinations, the product rotational polarization is reported using the quasiclassical trajectory method in the photoinitiated bimolecular reaction A + BC --> AB + C on attractive, mixed, and repulsive surfaces. Four polarization-dependent differential cross sections (PDDCS) which are sensitive to many photoinitiated bimolecular reaction experiments are presented. Furthermore, the dihedral angle distribution P(phi(r)) characterizing the K-K'-J' correlation and the distribution of angle between K and J' P(theta(r)) are discussed. Finally, the angular distributions P(theta(r),phi(r)) of product rotational vectors in the form of polar plots in theta(r) and phi(r) are shown.

The effect of axial ligand plane orientation on the contact and pseudocontact shifts of low-spin ferriheme proteins

Abstract: The effect of axial ligand nodal plane orientation on the contact and pseudocontact shifts of a symmetrical low-spin octamethylferriheme center has been calculated as a function of the angle of the axial ligand. Simple Huckel techniques have been used to estimate the contact contribution, and values obtained from model hemes, together with counter-rotation of the g-tensor, have been used to estimate the pseudocontact contribution, for the eight β-pyrrole methyl and four meso-H positions. It is found that the maximum and minimum contact shifts occur when the axial ligand is aligned at an angle of ±15° to the meso-H axes of the heme, rather than when the axial ligand plane lies along the porphyrin nitrogens, as assumed previously by some investigators. For systems having one planar axial ligand or two ligands in parallel planes, the contact and pseudocontact contributions at the meso-H positions are comparable in size (at least on the basis of simple Huckel estimates), while the contact contribution clearly dominates the isotropic shifts of the heme methyls. Allowing for the substituent effect of the 2,4-vinyls of protohemin, or the 2,4-thioethers of hemin c, as well as the average diamagnetic shifts of the heme methyls and meso-H, plots of the predicted shifts as a function of axial ligand nodal plane orientation have been constructed for hemin b- and c-containing proteins. Excellent agreement in the order of shifts, and reasonable agreement in the sizes of the observed shifts, is observed in the majority of the ferriheme proteins for which the methyl and meso-H resonances have been assigned and proton shifts reported. Plots have also been constructed for hemin c-containing proteins having the two axial ligand nodal planes oriented at relative angles of 40°, 70°, and 80°. Excellent agreement in the order of shifts, and reasonable agreement in the magnitudes of the observed shifts, is observed in all cases of bacterial cytochromes which do not fit the plots that assume the ligands are in parallel planes, except one – the cytochrome c-552 of Nitrosomonas europae. Except for this case, where the order of the predicted methyl shifts at any angle of the axial ligands disagrees with the observed, the reasons can usually be attributed to a large dihedral angle between two axial ligand nodal planes, to strong H-bonding interactions involving His and/or CN– ligands, or to off-axis binding of one (or both) axial ligand(s). Ruffling of the porphyrin ring may also contribute to the contact shift in as yet undefined ways. Hence, despite the simplicity of the calculations, the agreement with observed data is highly satisfying and the concept of the importance of axial ligand plane orientation on the observed proton shifts of heme proteins is fully confirmed.

Remarkable NLO response and infrared absorption in simple twisted molecular π-chromophores

Abstract: Computational modeling reveals that, by substitutional modification of interplanar dihedral angles in a series of quinopyrans, both the optical absorption cross section and the first hyperpolarizability can be widely tuned in both frequency and magnitude. This is a promising structural control scheme for modulating molecular nonlinear optical and infrared absorption properties. The maximum nonresonant μβ estimated for a tetraalkyl-substituted 4-quinopyran, the full AM1-optimized interplanar dihedral angle of which is 104°, is ∼70000 × 10-48 esu, at an excitation energy of 0.10 eV. This is 4 orders of magnitude larger than that of the archetypical NLO chromophore, 4-N,N‘-(dimethylamino)-4‘-nitrostilbene, at the same excitation frequency. The effects of conjugation pathway, strength of the electron donor/acceptor groups, and auxiliary donor and acceptor on the molecular response properties have also been analyzed. The optical absorption at a twist angle of 90°, when the molecule can be described as two disj...

Three-Bond C−O−C−C Spin-Coupling Constants in Carbohydrates: Development of a Karplus Relationship

Abstract: A range of 13C-labeled carbohydrates containing C−O−C−C coupling pathways having different structures and dihedral angles has been prepared and used to identify structural factors affecting 3JCOCC,...

Elucidation of the Chain Conformation in a Glassy Polyester, PET, by Two-Dimensional NMR

Abstract: The chain conformation of glassy poly(ethylene terephthalate) (PET) was characterized by two-dimensional double-quantum nuclear magnetic resonance (NMR). In amorphous carbon-13-labeled PET, the statistics of the O-13CH2-13CH2-O torsion angle were determined, on the basis of the distinct shapes of the two-dimensional NMR patterns of trans and gauche conformations. In crystalline PET, the trans content is 100 percent, but in the amorphous PET it is only 14 percent (+/-5 percent). An average gauche torsion angle of 70 degrees (+/-9 degrees) was obtained. Implications for materials properties of polyesters are discussed.

Why Does the Active Form of Galactose Oxidase Possess a Diamagnetic Ground State

Abstract: The relative orientation of the two magnetic orbitals, the CuII d x 2-y 2 orbital and the half-occupied π orbital of the tyrosyl radical, is the key to answering the question in the title. The arrangement shown (CuII -O-C bond angle of about 130° and a dihedral angle of about 90° between the x,y plane of the CuII polyhedron and the tyrosyl ring plane) leads to an overlap of the orbitals, which results in a singlet ground state.

A close look at dihedral angles and melt geometry in olivine-basalt aggregates: a TEM study

Abstract: Olivine-basalt aggregates sintered at high P/T have been used as a simplest approximation of partially molten upper mantle peridotite. In the past, geometry of partial melt in polycrystalline olivine (and other materials) has been characterised by dihedral (wetting) angles which depend upon surface free energy. However, since olivine (like most other crystalline materials) is distinctively anisotropic, the simple surface energy balance defining the dihedral angles cos(Θ/2)=gb/2sl is not valid and melt geometry is more complicated than can be expressed by a single dihedral angle value. We examine in detail melt geometry in aggregates held at high temperature and pressure for very long times (240–612 h). We show the simple dihedral angle concept to be invalid via transmission electron microscope images. Olivine-basalt interfaces are frequently planar crystal faces (F-faces) which are controlled by the crystal structure rather than the surface area minimisation used in the simple dihedral angle concept. Nevertheless, the dihedral angles may provide useful insights in some situations. They may give a rough estimation of the wetting behaviour of a system, or be used to approximate the melt distribution if F-faces are not present (possibly at large grain size and very low melt fraction). Our measurements, excluding F-faces, give a range of dihedral angle values from 0 to 10° which is significantly lower than reported previously (20–50°). The nature of 0° angles (films and layers up to 1 μm in thickness) is unclear but their frequency compared to dry grain boundaries depends on grain size and melt fraction (e.g. 70% for grain size 43 μm and melt fraction 2%).

Theoretical Studies of Steric Effects on Intraligand Electron Delocalization: Implications for the Temporal Evolution of MLCT Excited States

Abstract: The effect of steric bulk on electron delocalization in 4-arylpyridines has been studied by computational methods. Ab initio (HF, UHF, ROHF, MP2, UMP2, and ROMP2) as well as density functional theory (USVWN and UB-LYP) approaches were applied to a series of molecules and their corresponding anions. These molecules are put forth as models for the ground and MLCT excited states of three polypyridyl ligands that were the subject of a recent report on the effects of sterics and delocalization on the photophysics of several Ru II complexes (Damrauer, et al. J. Am. Chem. Soc.1997, 119, 8253). The present study finds that, in the series 4-phenylpyridine, 4-(o-tolyl)pyridine, and 4-(2,6-dimethylphenyl)pyridine, the steric effect of the ortho-methyl groups serves to increase the dihedral angle between the pyridyl and phenyl rings of the neutral compounds from ca. 45° in the case of 4-phenylpyridine to ca. 65° and 90° in the mono- and dimethylated compounds, respectively. These results are generally consistent with the single-crystal X-ray structures of the three corresponding bipyridines, also reported herein. Upon one-electron reduction, calculations on all three model ligands reveal a preference for a coplanar structure, with the optimized geometries reflecting a balance between an energetic stabilization gained via conjugation in the planar form and unfavorable steric interactions between the methyl group(s) of the 4-aryl substituent and the pyridyl protons ortho to the central C-C bond. Calculated dihedral angles were 0°,25°, and45° for 4-phenyl-, 4-(o-tolyl)-, and 4-(2,6dimethyl)pyridine, respectively. Finally, a simulation of the Franck -Condon state evolution of MLCT states of molecules containing the bipyridyl analogues of the three models was carried out by computing singlepoint energies of each compound as its monoanion in the optimized neutral geometry. Comparison of these energies with those of the fully optimized anions revealed effective reorganization energies of 4 -7 kcal/mol for 4-phenylpyridine, 4-7 kcal/mol for 4-(o-tolyl)pyridine, and ca. 6 kcal/mol for 4-(2,6-dimethylphenyl)pyridine. The implications of these results as they pertain to ultrafast spectroscopic studies of MLCT excitedstate evolution in the corresponding Ru II bipyridyl complexes are discussed.

Conformational Analysis (ab Initio HF/3-21G*) and Optical Properties of Symmetrically Disubstituted Terthiophenes

Abstract: We report a conformational analysis of several substituted terthiophenes using ab initio calculations performed at the HF/3-21G* level. Geometries of terthiophenes having methoxy substituents in 3,3‘‘ positions (DMOTT), methyl groups in the same positions (DMTT), and ethyl substituents in 3‘,4‘ positions (DETT) are compared with that of the unsubstituted molecule (TT). For all these symmetrical molecules, it is observed that the two dihedral angles are independent of each other. The most stable conformation of TT is found for dihedral angles θ = φ = 147.2°, whereas three maxima are located at 0°, 90°, and 180°. The insertion of methoxy groups in 3,3‘‘ positions favors a more planar conformation with a higher rotational barrier at 90°. This behavior is explained by the electron donor properties of the methoxy groups. By contrast, the addition of two methyl groups at the same positions induces a twisting in the molecule which is caused by the steric hindrance between the methyl substituents and the sulfur a...

Structural studies of bis-catecholate, bis-dithiocatecholate, and tetraalkoxy diborane(4) compounds

Abstract: X-ray structures are described for the bis-catecholate, bis-dithiocatecholate, and tetraalkoxy diborane(4) compounds B2(1,2-O2C6H4)2 (1), B2(1,2-O2-4-ButC6H3)2 (2), B2(1,2-O2-3,5-But2C6H2)2 (3), B2(1,2-S2C6H4)2 (4), B2(1,2-S2-4-MeC6H3)2 (5), and B2(OCH2CMe2CH2O)2 (6). All the compounds adopt structures in the solid-state in which the B2O4 or B2S4 units are planar or very nearly so. In compounds 2 and 3, the dihedral angles between the two BO2C2 planes are 17.3 and 31.8° respectively whereas in 1, 4 and 5 these angles are exactly 0°. In 6, a 3-fold disorder precluded our obtaining accurate positions for the two boron atoms, yet a dihedral angle of 0° is required by the 3 site symmetry. The structure of the bis(Lewis base) adduct of B2Cl4, [B2Cl4(NHMe2)2] (7), is also described and structures of the salt [NH2Me2][B(1,2-O2C6H4)2] (8) and the NMe2-bridged dimer [{BCl2(μ-NMe2)}2] (9) are available in the Supporting Information. Compound 1 crystallized in the monoclinic space group P21/c with a = 4.746(1) A, b...

Preferred Conformation of C-Lactose at the Free and Peanut Lectin Bound States

Abstract: A conformational analysis of methyl -C-lactoside (5) is carried out (Table 1), which suggests the preferred solution conformation of 5 to be described as a mixture of conformers A ( = 300; = 60) and B ( = 300; = 300) to a first approximation. Applying a modified Karplus equation for the vicinal coupling constants observed for the H.a and H.1' protons of 5, the dihedral angle ( = O.5'-C.1'-C.a-C.4) was deduced to be approximately +280. Nuclear Overhauser effect (NOE) experiments were then conducted on 5-D2 and its parent methyl -O-lactoside in a 7:3 mixture of pyridine-d5 and methanol-d4, qualitatively demonstrating that the conformational characteristics of both methyl -C- and -O-lactosides at the free states are represented as a mixture of two conformers A and B, but their relative population may be different. Through X-ray analysis, it has been definitively established that the conformation ( = 297(7) and = 120(2)) of C-lactose bound to peanut lectin is practically identical to the conformation ( = 291(6) and = 118(9)) of its parent O-lactose bound to the same protein.

Is a Transition State Planar or Nonplanar in Oxidative Additions of C−H, Si−H, C−C, and Si−C σ-Bonds to Pt(PH3)2? A Theoretical Study

Abstract: A theoretical study of oxidative additions of H−CH3, CH3−CH3, H−SiR3, and SiR3−CH3 (RH, Cl, or Me) to Pt(PH3)2 was carried out with ab initio MO/MP2-MP4SDQ, CCD, and CCSD methods. The oxidative addition reactions of C−H and Si−H σ-bonds occur through a planar transition state (TS) structure, in accordance with the expectation from an orbital interaction diagram. However, the oxidative addition reactions of CH3−CH3 and SiH3−CH3 take place through a nonplanar TS structure, unexpectedly; the dihedral angle δ between PtP2 and PtXC planes (X = C or Si) is about 70° for X = Si and about 80° for X = C. Intrinsic reaction coordinate calculation of the SiH3−CH3 oxidative addition clearly indicated that this nonplanar TS is smoothly connected to the planar product on the singlet surface. The dihedral angle δ at the TS is larger in the SiMe3−CH3 and SiCl3−CH3 oxidative additions than that in the SiH3−CH3 oxidative addition. Electron distribution in the TS and effects of bulky substituent on the dihedral angle sugges...

Packing of Hydrocarbon Chains and Symmetry of Condensed Phases in Langmuir Monolayers

Abstract: We compare the packing characteristics of alkyl chains in Langmuir monolayers of nonchiral and racemic compounds as determined from available grazing incidence X-ray diffraction data. The analysis demonstrates a gradual change of the projected unit cell dimensions from those of a hexagonal packing of hydrocarbon chains, characteristic of high-temperature monolayer phases, to one of two more dense rectangular packing modes with the projected unit cell dimensions 5.0 × 7.5 A2 and 4.4 × 8.7 A2, characteristic of low-temperature phases. The 5.0 × 7.5 A2 unit cell incorporates the well-known herringbone arrangement, with an ideally 90° dihedral angle between the planes of carbon backbone chains. The 4.4 × 8.7 A2 cell, almost never observed in 3D structures, is characterized by a 40° dihedral angle. We characterize the packing modes by lattice energy calculations. The distribution of the projected unit cell dimensions for the various Langmuir monolayers reveals no discontinuity in the local molecular order betw...

Absolute sense of twist of the c12-c13 bond of the retinal chromophore in rhodopsin : semiempirical and nonempirical calculations of chiroptical data

Abstract: The sign of the dihedral angle of the 12-s-trans bonds in the protonated Schiff base of 11-cis-retinal (see picture on the right) correlates with the sign of the long-wavelength absorption in the circular dichroism spectra. This is the result of the high-quality excited-state calculations on the chromophore of the visual pigment rhodopsin.

Structural studies of Impatiens balsamina antimicrobial protein (Ib-AMP1).

Abstract: Structural studies of Ib-AMP1, a small antimicrobial peptide derived from the seeds of Impatiens balsamina have been performed using circular dichroism (CD) and two-dimensional proton nuclear magnetic resonance (1H NMR). This 20-residue peptide is highly basic with five arginine residues and contains four cysteines which form two intramolecular disulfide bonds. CD results reveal that the peptide may include a beta-turn but do not show evidence for either helical or beta-sheet structure over a range of temperature and pH. Structural information from NMR was obtained in the form of proton-proton internuclear distances inferred from NOEs and dihedral angle restraints from spin-spin coupling constants, which were used for distance geometry calculations. Owing to the difficulty in obtaining the correct disulfide connectivities by chemical methods, three separate calculations were performed; with no disulfides and with the two possible alternate disulfide connectivities. Results from distance geometry calculations reveal that although the peptide is small, the cysteines constrain part of it to adopt a well-defined main chain conformation. From residue 6 to 20, the backbone is well defined, whilst the N-terminal region, residues 1-5, has very few constraints and appears to be very flexible. In the defined core region, there are three beta-turns at residues 9-12, 10-13, and 12-15. The side chains show no strong interactions in the NMR spectra and are therefore thought to adopt multiple conformations. Superposition of the structures generated shows that the peptide has two hydrophilic patches which are at opposite ends of the molecule separated by a large hydrophobic patch. Little is known about the mode of action of this protein, but it is thought to interact with a membrane-bound receptor, and possible sites of interaction are discussed. The structures determined are compared with those of the alpha-conotoxins, which are also highly basic proteins with similar disulfide connectivities.

Molecular and electronic structures of heteroaromatic oligomers : model compounds of polymers with quantum-well structures

Abstract: Conformational preferences of 2,2‘-bithiophene, 2-(2-thienyl)pyrrole, and N-methyl-2-(2-thienyl)pyrrole have been investigated by means of computational methods. Calculations were performed at the ab initio HF/6-31G(d) and MP2/6-31G(d) levels and, additionally, with the density functional B3-LYP/6-31G(d). The results indicate that 2-(2-thienyl)pyrrole behaves similarly to the 2,2‘-bithiophene. Thus, two minimum energy conformations were found for each compound, which correspond to anti-gauche and syn-gauche. Such minima are separated by barriers of about 1.7 and 1.3 kcal/mol at the HF and MP2 levels. On the contrary, the preferences found for N-methyl-2-(2-thienyl)pyrrole were different, giving an almost negligible energy barrier between the two minimum energy conformations. Furthermore, at the MP2 level the anti-gauche and syn-gauche minimum energy conformations present an inter-ring dihedral of 135° and 68°, respectively, displaying deviations greater than those found in 2,2‘-bithiophene and 2-(2-thieny...

Determination of Free Energy of δ-Ferrite/γ-Austenite Interphase Boundary of Low Carbon Steels by In-situ Observation

Abstract: Phase transformations of δ-ferrite/γ-austenite in low carbon steels containing 0.017 mass% phosphorus are observed in-situ by using a combination of confocal scanning laser microscope with infrared image furnace. Dihedral angles at triple points of one high energy δ/δ grain boundary and two incoherent δ/γ interphase boundaries are measured by holding the sample at temperatures where δ- and γ-phases co-exist in quasi-equilibrium. From the average value of observed dihedral angles, free energy of γ/δ incoherent boundary for a steel with low sulfur content (0.007 mass%) is estimated to be 0.450 J/m2 at ca. 1700 K. The effects of temperature and sulfur content on the dihedral angle and free energy of incoherent δ/γ boundary are also discussed.

Nanorheology of molecularly thin films of n-hexadecane in Couette shear flow by molecular dynamics simulation

Abstract: In this work the rheological and structural properties of n-hexadecane have been studied by molecular dynamics simulation. The model consists of two structured atomic walls between which the fluid is sheared by moving the walls in opposite directions. The fluid consists of chains of n-hexadecane molecules. Each molecule has 16 interaction sites where each site on the molecule represents a CH2 or CH3 group. The Lennard–Jones potential governs the intermolecular interactions. Stretching, angular and torsional potentials are used for the intramolecular interactions to preserve the integrity of the molecules. An isothermal simulation of the Couette shear flow is conducted to reveal the rheological properties of n-hexadecane at high Weissenberg numbers in films as thin as 1 nm. The results obtained show an increase in the average viscosity of hexadecane as the film thickness is decreased to scales comparable to the molecular diameter of the chain segments. These results agree with recent experimental findings for very thin films, revealing shear thinning and normal stress difference effects which are an indication of non-Newtonian behaviour. Structural properties such as the density profiles, bond angle and dihedral angle distribution functions and average end-to-end distance of the molecules are obtained for films of different thickness and at different shear rates. The effects of the wall–fluid interaction strength on the fluid properties are also investigated in different adsorption limits. It seems that adsorption is a determining factor in the properties of these ultrathin films. The results indicate different shear responses depending on the adsorption limit of the surface.

Determination of the Protein Backbone Dihedral Angle ψ from a Combination of NMR-Derived Cross-Correlation Spin Relaxation Rates

Abstract: A sensitive triple resonance NMR experiment is presented for the measurement of the protein backbone dihedral angle ψ based on cross-correlated spin relaxation between 13Cα−1Hα and 15N−1HN dipolar interactions in 15N,13C-labeled proteins. In general, as many as four ψ values can be consistent with a single cross-correlation rate. However, in many cases, the ambiguity can be significantly reduced (for example, from four to two) when a combination of cross-correlation relaxation rates are employed. This is illustrated by considering rates derived from 13Cα−1Hα/15N−1HN dipolar and from 13Cα−1Hα dipolar/carbonyl chemical shift anisotropy relaxation mechanisms for the proteins ubiquitin and CheY. Using a database of ψ values obtained from high-resolution X-ray structures, it is shown that for values in the range −50° ≤ ψ ≤ 40° a single ψ can be obtained to high probability.

Shape distortion in liquid-phase-sintered tungsten heavy alloys

Abstract: Shape retention during liquid phase sintering is a major concern at high liquid contents, or large density differences between the solid and the liquid phases. This study demonstrates the role of microstructural parameters in controlling the bulk dimensional changes that occur during liquid phase sintering of tungsten heavy alloys (WHAs). Tungsten-nickel-copper alloys containing 80 wt pct tungsten, the balance containing Ni and Cu in the ratio 6:4, 7:3, or 8:2, were sintered at temperatures between 1400 °C and 1500 °C. Compact distortion was quantified using a coordinate measuring machine and related to the microstructural parameters, such as solid volume fraction, grain size, dihedral angle, grain continguity, and connectivity. Supplementary experiments were performed on W-Ni, W-Cu, and Mo-Cu alloys to compare the role of microstructural parameters in controlling distortion. A low solid solubility and a small grain size coupled with a high dihedral angle and connectivity restrict distortion. Based on the experimental observations and stereological relations, the critical solid content required to maintain structural rigidity is related to specific combinations of dihedral angle and grain connectivity.

Density functional study on the structures and vibrational spectra of the radical anion and cation of biphenyl

Abstract: Density functional theory using the 6–31G ∗ basis set and two non-local exchange-correlation functionals (B-YLP and B3-LYP) has been applied to the calculations of the structures and vibrational spectra of the radical anion and cation, of biphenyl. The B3-LYP dihedral angles between the two phenyl rings are 5.8 ° and 19.5 ° for the radical anion and cation respectively. Upon ionization, structural changes occur in the direction from benzenoid to quinoid. The unsealed vibrational frequencies calculated at the B-YLP/6–31G ∗ level are mostly in agreement with the frequencies in the Raman spectra of the radical anion and cation of the normal and perdeuterated species reported in the literature. The calculations predict that both the radical anion and cation give rise to a very strong infrared band, and that this band arises from a mode in which the benzenoid-to-quinoid deformation occurs out of phase in the two phenyl rings.

Solution structure of an intramolecular DNA triplex linked by hexakis(ethylene glycol) units: d(AGAGAGAA-(EG)6-TTCTCTCT-(EG)6-TCTCTCTT).

Abstract: A DNA molecule was designed and synthesized with three octanucleotide stretches linked by two hexakis(ethylene glycol) chains to form an intramolecular triplex in solution. The structural data obtained from a series of NMR NOESY spectra yielded interproton distances, and COSY experiments provided dihedral angle information for analysis of deoxyribose ring pucker. Using distance geometry followed by simulated annealing with restrained molecular dynamics and relaxation matrix refinement, a well-refined ensemble of conformations was calculated. Although some NOE cross-peaks involving protons of the hexakis(ethylene glycol) linker could be identified, most could not be assigned and the conformations of the linkers were not determined. The deoxyribose conformations are predominantly of the S type, except for the protonated cytosine residues in the third strand which show hybrid N and S character. Overall, the duplex part of the molecule resembles a B-DNA double helix with the third strand bound in its major gr...