Showing papers on "Dihedral angle published in 1990"

Reaction path study of conformational transitions in flexible systems: Applications to peptides

Abstract: A new protocol to find minima and transition states in flexible systems is proposed. It is tested on alanine dipeptide (AD) with four minima and eight transition states and applied to a flexible molecule, isobutyryl–(ala)3–NH–methyl (IAN), the shortest peptide which can form a full helical turn. There were found 138 minima and 490 transition states for IAN. It is shown that the connectivity network between the minima is very dilute and composed of transitions localized on one or two neighboring amide units. Most of the transitions involve one or two dihedral flips. The reaction coordinate from an extended chain conformation to a helix follows a sequence of nonoverlapping rotations around bonds. The rotations along the reaction coordinates are such that the hard repulsions between different atoms are minimized but at the same time the hydrogen bonding and the electrostatic interactions are maximized. A melting‐like transition which is associated with the sudden opening of a large number of hopping channels is identified between minima at approximately 5 kcal/mol above the lowest energy minimum. The calculated minima and transition states are used to construct a master equation for the two molecules. The vibrational spectrum of the N–H stretch as a function of time and temperature is finally calculated. It is demonstrated that time‐dependent lineshape analysis can be a useful tool to investigate the properties of the large number of minima and the intervening transitions.

The effect of conformation on the CD of interacting helices: A theoretical study of tropomyosin

Abstract: A recent report [M. E. Holtzer, et al. (1988) Biophysics Journal, 53, 96a] of the anomalous CD spectrum of the tropomyosin (TM) fragment 11TM127 motivated us to model the system as two 21-residue alpha-helices distorted to a coiled-coil conformation. We used strong-coupling exciton theory to model the optical properties of the system. Two backbone amide excited states (n pi* and pi pi*) were considered, as well as four excited states (Lb, La, Bb, Ba) for the phenolic side chain. We calculated the effect of superhelix formation on the backbone CD spectrum. The decrease in molar ellipticity of the alpha-helix parallel-polarized transition at 208 nm was found to be a simple function of superhelix tilt angle. We then modeled a coiled coil (radius = 5.5 A, pitch = -140 A) with one aromatic ring per superhelix. Steric interactions between aromatic side chains in a coiled coil were calculated as a function of side-chain conformation and heptet position. Steric interactions between phenolic rings will be significant for heptet positions a and d, but not for positions b, c, e, f, or g. We calculated the phenolic Lb transition rotational strength as a function of position within the heptet repeats, and of all possible side-chain dihedral angles, chi 1 and chi 2. When tyrosines were placed at heptet positions b, c, e, f, or g, the rotational-strength surface was nearly identical to that of a single tyrosine in an undistorted helix. In contrast, the rotational-strength surface for tyrosines in heptet positions a or d showed substantial intertyrosine coupling components. The rotational-strength surfaces for the three types of heptet positions (position a, position d, and the others) allowed an interpretation of the aromatic CD spectra of TM and its fragments. It was predicted that the three types of heptet positions will be spectroscopically distinguishable.

Role of ring torsion angle in polyaniline: Electronic structure and defect states

Abstract: The role of phenyl-ring torsion angle in determining the nature of the ground and charged-defect states of polyaniline is explored. The coupling of the transfer integral between nitrogen atom and phenyl-ring constituents of the polyaniline chain to the dihedral angle of the rings competes with the substantial steric repulsion between adjacent rings in determining the conformation of these systems. The ring conformation of the leucoemeraldine-base (LB) form of polyaniline is described by a novel ring-torsion-angle order parameter. The anharmonicity of the interring steric potential leads to a temperature-dependent mean order parameter, and thus to the prediction of thermochromic effects consistent with experiment. Furthermore, changes in optical spectra accompanying derivatization of the rings can be understood by the response of the substituted polymer to modifications of the steric potential. The existence of two degenerate ring-torsion-angle phases in LB implies that both polaronic and solitonic ring-angle-alternation defect states may be relevant in describing the charged states in polyaniline. As these defects involve substantial changes in ring torsion angle, they are expected to possess large kinetic mass, in agreement with photoinduced absorption experiments on polyaniline. The anticipated Peierls ground state of the oxidized pernigraniline-base form of polyaniline can be regarded in part as a ring-torsion-angle dimerized state; consequently, the charge states of this material are also expected to be massive defects in the ring-rotational order. The importance of ring rotations in other ring-containing electronic polymers, such as poly(paraphenylene sulfide), is discussed.

Solution structure of phage .lambda. half-operator DNA by use of NMR, restrained molecular dynamics, and NOE-based refinement

Abstract: The structure of a DNA decamer comprising the left half of the O{sub R}3 operator from bacteriophage {lambda} is determined in solution by using nuclear magnetic resonance spectroscopy and restrained molecular mechanics calculations. Nuclear magnetic resonance assignments for nonexchangeable protons are obtained by two-dimensional correlated and nuclear Overhauser effect (NOE) spectroscopies. Exchangeable proton resonances are assigned by one-dimensional NOE experiments. Coupling constant measurements from one- and two-dimensional experiments are used to determine approximate dihedral angles within the deoxyribose ring. Distances between protons are estimated by extrapolating distances derived from the time-dependent NOE intensities to initial mixing times. The sets of dihedral angles and distances form a basis for structure determination by restrained molecular dynamics. Separate runs start from classical A and from B DNA and converge to essentially identical structures (atomic root mean square difference of 0.8 {angstrom}). The structures are improved by NOE-based refinement in which observed NOE intensities are compared to those calculated by using a full matrix analysis procedure. Final NOE residual (R) factors were less than 0.19. The resultant structures are generally B type in character, but display local sequence-dependent variations in dihedral angles and in the spatial arrangement of adjacent base pairs. Although the entiremore » structure exhibits a small bend, the central core of the half-operator, which comprises the sequence-specific recognition site for cro repressor, is straight.« less

13C, 1H spin–spin coupling. X—Norbornane: A reinvestigation of the karplus curve for 3J(13C, 1H)

Abstract: 13C, 2H spin–spin coupling constants over one, two and three bonds were measured from the 100-MHz 13C NMR spectra of deuteriated isotopomers of norbornane-d1, (1) and fenchane-2-d1 (2) and also of a number of mono-deuteriated alkyl-substituted adamantanes. The magnitudes of the corresponding J(13C, 1H) values derived from these data by application of the well known relationship J(X, 1H) = 6.5144J(X, 2H) are discussed with respect to the structural data for the hydrocarbons, which were taken from force field calculations with the Allinger MM2 method. In particular, the dihedral angle dependence and the Karplus curve for 3J(13C, 1H) are investigated. Coupling constants calculated by the FP-INDO method are compared with the experimental data, and the effect of substitution by additional CC bonds in α-, β- and γ-positions of the 13C-αC-βC-γH bond fragment is elucidated. If substituent effects that arise through branching and methyl substitution in 1 and 2 are taken into account for dihedral angles ϕ > 90°, one derives 3J(13C, 1H) = 4.50 − 0.87 cos ϕ + 4.03 cos 2ϕ with J(0°) = 7.7, J(60°;) = 2.0 and J(180°) = 9.4 Hz.

Crystal structure and electronic properties of dibromo- and dichloro-tetrakis[µ3-bis(2-pyridyl)amido]tricopper(II) hydrate

Abstract: The crystal structures of [Cu3(bipyam–H)4Cl2]·H2O (1) and [Cu3(bipyam–H)4Br2]·H2O (2) where bipyam–H = bis(2-pyridyl)amide, have been determined by X-ray analysis, in the orthorhrombic space group Pnn2: (1), a= 14.092(3), b= 12.895(3), (c)= 11.190(2)A, Z= 2, and R= 0.032 for 2 453 observed and 2 029 unique reflections; (2), a= 14.186(3), b= 13.040(3), c= 11.313(2)A, Z= 2, and R= 0.043 for 1 574 observed and 1 465 unique reflections. The two structures are isomorphous with near isostructural [Cu3(bipyam–H)4X2] units in special positions of two-fold symmetry and a non-co-ordinated water molecule. The Cu3N12X2 chromophores involve nearly linear Cu3 units, Cu–Cu–Cu 178.4°(mean), terminated by the two halide anions. The four separate bipyam–H ligands act as tridentate ligands, involving co-ordination to the three separate copper(II) ions, with Cu–Cu distances of 2.471(1) and 2.468(1)A, for (1) and (2), respectively. If the Cu–Cu separations are ignored, the central Cu atom in both structures involves a four-co-ordinate rhombic coplanar CuN4 chromophore generated by the central amido nitrogens of the four bipyam–H ligands. The two terminal Cu atoms involve a square-based pyramidal CuN4X chromophore, generated by the terminal pyridine nitrogens of the four bipyam–H ligands and an axial halide anion. An average dihedral angle of 48° is involved between the planes of the pyridine rings of the individual bipyam–H ligands, which results in a spiral configuration of the [Cu3(bipyam–H)4X2] units. The spin-only magnetic moment of complex (1) is ca. 1.40 B.M. per Cu atom, consistent with antiferromagnetic coupling between the copper(II) atoms of the trimer. Both complexes are e.s.r. silent, again consistent with strong antiferromagnetic coupling. The electronic spectra of (1) and (2) have a band maximum at 15 500 cm–1, with a high-energy shoulder at 19 230 cm–1, consistent with the two different stereochemistries present.

Molecular-dynamics simulation of crystalline 18-crown-6: thermal shortening of covalent bonds

Abstract: Molecular-dynamics simulations of crystalline 18-crown-6 have been performed in a study of the apparent thermal shortening of covalent bonds observed in crystal structures. At 100 K, a shortening of 0.006 _+ 0.001 A for C----C and C----O bonds was obtained. This result was found to be independent of details of the force field and the simulation. There was agreement between computational and experimental values for the thermal parameters, as well as for the molecular geometry (bond and dihedral angles) of 18-crown-6. Some differences are attributed to the inability of the force field to reproduce hydrogen-bonding geometries. Simulation at 295 K resulted in an estimated shortening of 0.019_+ 0.005 A. Thus at room temperature for C--C bonds (apparent) thermal shortening and (real) chemical shortening, resulting from the electronegative oxygen substituents, are of the same order of magnitude. In the simulation at 295 K occasional dihedral transitions were observed, which may reflect the proximity of the melting point (312 K).

Molecular-dynamics simulation of crystalline 18- crown-6:* Thermal shortening of covalent bonds.

Abstract: Molecular-dynamics simulations of crystalline 18-crown-6 have been performed in a study of the apparent thermal shortening of covalent bonds observed in crystal structures. At 100 K, a shortening of 0.006 _+ 0.001 A for C----C and C----O bonds was obtained. This result was found to be independent of details of the force field and the simulation. There was agreement between computational and experimental values for the thermal parameters, as well as for the molecular geometry (bond and dihedral angles) of 18-crown-6. Some differences are attributed to the inability of the force field to reproduce hydrogen-bonding geometries. Simulation at 295 K resulted in an estimated shortening of 0.019_+ 0.005 A. Thus at room temperature for C--C bonds (apparent) thermal shortening and (real) chemical shortening, resulting from the electronegative oxygen substituents, are of the same order of magnitude. In the simulation at 295 K occasional dihedral transitions were observed, which may reflect the proximity of the melting point (312 K).

Medium-range order in v-SiO2

Abstract: A computer algorithm has been developed to generate fully valence-satisfied models of amorphous AX 2 chemically ordered continuous random networks. The specific application here is the successive addition of rigid corner-sharing AX 4 tetrahedral units and the networks produced are analyzed with reference to the structure of v-SiO 2 . Control over parameters such as bond angles, minimum ring size and dihedral angle is possible while short-range order is ensured by using rigid AX 4 tetrahedral units as the basic building block. Models have been generated to investigate a region of parameter space with minimum ring size and equilibrium SiOSi bond angles as variables. Careful considerations is given to the effects of experimental resolution, thermal broadening and finite model-size correction when comparing the models with experimental data. It is found that a comparatively narrow region of parameter space gives rise to good models assessed in terms of their fit to experimentally derived real-space distribution functions, bond-angle distributions, reciprocal space scattering data and, in particular, the relative intensity of the first sharp diffraction peak (FSDP).

The shape and stability of liquid menisci at solid edges

Abstract: The shape and stability of liquid menisci attached to a solid edge with dihedral angle 2α is investigated. It is shown that in addition to the family of cylindrical menisci a family of azimuthally modified unduloids exists. A double Fourier series of the latter with respect to their axis (parallel to the extension of the edge) and with respect to the azimuth is derived. The dispersion relation between the axial wavenumber q, the azimuthal wavenumber s and the waviness parameter d is calculated. When the condition of constant contact angle γ along the contact lines with the solid is applied, a one-dimensional family of modified unduloids fitting to the edge is obtained. Their axial wavenumber q becomes independent of the waviness d at the bifurcation with the family of cylindrical menisci, such that this bifurcation limits the stability. The respective stability criteria are derived and evaluated. For α + γ > ½π the cylindrical menisci are convex. They reveal a maximum stable length, which quadratically tends to infinity when α + γ = ½π is approached. The smallest stable extension arises for the free cylindrical column (the Rayleigh jet), which is covered by the present investigations by assuming α = π, γ = ½π. For α + γ < ½π the cylindrical menisci are concave and stable: no bifurcation with the family of modified unduloids arises.

On the use of conformationally dependent geometry trends from Ab Initio dipeptide studies to refine potentials for the empirical force field CHARMM

Abstract: Previous 4-21G ab initio geometry optimizations of various conformations of the model dipeptides (N-acetyl N'methyl amides) of glycine (GLY) and the alanine (ALA) have been used to help refine the empirical force constants and equilibrium geometry in the CHARMM force field for peptides. Conformationally dependent geometry trends from ab initio calculations and positions of energy minima on the ab initio energy surfaces have been used as guides in the parameter refinement, leading to modifications in the bond stretch, angle bending, and some torsional parameters. Preliminary results obtained with these refined empirical parameters are presented for the protein Crambin. Results for the cyclic (Ala-Pro-DPhe)2 are compared with those from other calculations. It seems that the dihedral angle fit achieved by the new parameters is significantly improved compared with results from force fields whose derivation does not include ab initio geometry trends.

Evaluation of molecular mechanics methods for the calculation of the barriers to planarity and pseudorotation of small ring molecules

Abstract: Molecular mechanics (MM2) methods have been utilized to estimate the barriers to planarity and/or pseudorotation for 23 small ring molecules. These methods were also used to calculate the structural parameters for different conformations of each molecule. In the case of four- and pseudo-four-membered rings (five-membered rings with double bonds), MM2 predicts the structure (dihedral angle) of the equilibrium conformation with good accuracy and does reasonably well in predicting barriers to planarity.

The thermodynamics of solvophobic effects: A molecular‐dynamics study of n‐butane in carbon tetrachloride and water

Abstract: We have carried out molecular‐dynamics simulations with holonomic dihedral angle constraints on two models of n‐butane in CCl4 and in water to study the effects of apolar and polar solvents on the gauche‐trans equilibrium. We calculated distributions of conformers from the torsional free‐energy surfaces for each model of butane in both solvents. For a four‐atom model of butane, the gauche‐trans equilibrium constant in either solvent is unchanged relative to its gas‐phase value. For an all‐atom model of butane, the equilibrium population of gauche conformers is increased relative to its gas‐phase value by 14% and 31% in CCl4 and water, respectively. The all‐atom results are consistent with the idea of solvophobic stabilization of the gauche conformation. We also computed finite‐difference temperature derivatives of the free energy to determine its energetic and entropic components. The gauche conformer of the four‐atom model is stabilized by entropy and destabilized by energy in CCl4. We find the opposite thermodynamic driving forces for the all‐atom model in CCl4. The gauche conformer is favored entropically and opposed energetically for both models in water. This result supports the idea that the butane hydrophobic effect is a manifestation of the hydrophobic interaction. Average interaction energies show that changes in solute–solvent interactions contribute significantly to the trans‐gauche internal energy differences in CCl4, while the internal energy differences in water are dominated by changes in the solvent–solvent interactions. Solvent–solute radial distribution functions show that CCl4 packing around the butane molecular is similar to that around other CCl4 molecules, and it is not sensitive to the butane conformation. The water distributions around the butane molecule are very flat, but they show that the water is more disordered around the gauche conformer than the trans.

Three-dimensional structure of porcine C5adesArg from 1H nuclear magnetic resonance data.

Abstract: Two-dimensional nuclear magnetic resonance spectra of porcine C5a{sub desArg} (73 residues) have been used to construct a list of 34 hydrogen bonds, 27 dihedral angle constraints, and 151 distance constraints, derived from nuclear Overhauser effect data. These constraints were used in restrained molecular dynamics calculations on residues 1-65 of C5a, starting from a folded structure modeled on the crystal structure of a homologous protein, C3a. Forty-one structures have been calculated, which fall into three similar families with few violations of the imposed constraints. Structures in the most populated family have a root-mean-square deviation from the average structure of 1.02 {angstrom} for the C{sup {alpha}} atoms, with good definition of the internal residues. There is good agreement between the calculated structures and other nuclear magnetic resonance data. The structure is very similar to that recently reported for human C5a. Some biological implications of these structures are discussed.

Primary sequence dependence of conformation in oligomannose oligosaccharides.

Abstract: The oligomannose series of oligosaccharides from bovine thyroglobulin (BTG) and the variant surface glycoprotein (VSG) ofTrypanosoma brucei have been isolated and sequenced by1H NMR. The structure of Man9GlcNAc2, the parent molecule of the series, is shown below. Structural isomerism occurs within this series through the removal of residues D1, D2, D3, and C. Using spin-spin coupling and chemical shift data the rotamer distributions about the dihedral angle ω for the Manα1-6Man\ and Manα1-6Manα linkages were determined for each member of the series. It is shown that the dihedral angle ω of the Manα1-6Man\ linkage exhibits low flexibility with a preference for the ω = 180° conformation when residue D2 is present and high flexibility when this residue is absent. Flexibility of ω for the Manα1-6Manα is largely independent of primary sequence and is intermediate between the two Manoα1-6Man\ extremes, again with a preference for the ω = 180° conformation. Open image in new window There are, however, data which indicate that removal of residue D3 may confer additional flexibility upon the dihedral angle ω of the Manα1-6Manα linkage. Molecular graphics modelling, together with chemical and enzymatic modification studies, suggest that the origin of the observed primary sequence dependence of the Manα1-6Man\ linkage arises from steric factors. On the basis of these observations taken together with previous work, it is postulated that recognition of individual oligomannose conformations may play a role in the control of N-linked oligosaccharide biosynthesis.

A tetrahedral zinc(II) complex of N-(R)-1-phenylethylsalicylideneimine. Structural and circular dichroism spectral investigations on stereoselectivity

Abstract: The stereoselectivity of bis[N-(R)-1-phenylethylsalicylideneiminato]zinc(II) has been studied by means of single-crystal X-ray analysis and circular dichroism (c.d.) spectra. The complex crystallizes in space group P212121 with a= 17.738(4), b= 29.632(9), c= 9.968(2)A, and Z= 4. The unit cell is comprised of four units each containing two complex molecules (A and B). Each molecule adopts a nearly tetrahedral structure with two bidentate ligands; the dihedral angle defined by the two chelate rings is 81.7° for molecule A and 84.9° for molecule B. The absolute configuration along the pseudo-C2 axis is Λ for both molecules. Based on the X-ray analysis it is suggested that intramolecular non-covalent interactions between the chiral N-substituent and the adjacent chelate ring give rise to stereoselectivity and the Λ configuration around the metal ion. The c.d. couplet (+and – signs) induced at the azomethine π–π* transition at around 27 000 cm–1 is discussed with respect to the absolute configuration and in comparison with the spectra of related Schiff-base complexes.

Molecular Structure of the Complex Formed Between the Anticancer Drug Cisplatin and d(pGpG): C2221 Crystal Form

Abstract: The three dimensional molecular structure of the adduct formed between the anticancer drug cisplatin and a DNA dinucleotide d(pGpG) has been determined by x-ray diffraction analysis at 1.37 A resolution and refined to a final R-factor of 0.11. This structure, solved by using data from a previously reported crystal form in the space group C2221, resembles that found in the space group P21212 (Sherman, et al., Science, 230, 412–417, 1985; ibid, J. Amer. Chem. Soc. 110, 7368–7381, 1988). In both structures, four crystallographically independent cis-[Pt(NH3)2 {d(pGpG)}] molecules aggregate into a tetrameric cluster that is stabilized by a large number of intermolecular hydrogen bonds and base-base stacking interactions. In each molecule, the platinum atom is coordinated to the N7 atoms of two guanine bases arranged in a head-to-head orientation, resulting in a large dihedral angle between the guanines. Intermolecular guanine-guanine base pairings between different intrastrand crosslinked molecules ar...

Poly(p-phenylene-co-2,5-pyrazine): An AM1 investigation

Abstract: We present an AM1 study of the geometry of some oligomers of a new electrically conductive polymer: the poly(p-phenylene-co-2,5-pyrazine) (PPPz). We examine the evolution of the total energy, the ionization potential and the inter-ring bond length as a function of the torsion angle between adjacent rings. We have also investigated the geometry of charged (ions +1 and −1) oligomers of PPPz. Based on the obtained results we can explain the observed increase in the conductivity for PPPz induced by p doping and we suggest a way of increasing its value.

Intramolecular interactions in N-vinyl-2-arylpyrroles and -2-heteroarylpyrroles by 1H and 13C NMR

Abstract: The introduction of a substituent in the 3-position of the pyrrole ring in N-vinyl-2-arylpyrroles and -2-heteroarylpyrroles results in an increase in the dihedral angles between the planes of the pyrrole ring and the aryl (or heteroaryl) residue, and a decrease in the dihedral angle between the planes of the pyrrole ring and the vinyl group. Introduction of the substituent in the 5-position of the pyrrole ring has the opposite effect on these angles. For N-vinyl-2-(2′-furyl)pyrrole, some spectral data suggest the formation of a CH…O hydrogen bond between the α-hydrogen atom of the vinyl group and the oxygen atom of the furyl ring. This is in accord with the results of quantum chemical calculations.

Motions of an α-helical polypeptide: Comparison of molecular and harmonic dynamics

Abstract: Molecular and harmonic dynamics simulations have been performed for a decaglycine α-helix. The extent of anharmonicity for various observables is studied by a direct comparison of the two types of simulations, at temperatures ranging from 5 to 300 K. The fluctuations of the cartesian, internal and normal mode coordinates, and their time dependence, are analyzed. The heat capacity of the α-helix is evaluated both from the temperature response of the system to an energy perturbation and from the fluctuations in the temperature of the system. It is shown that the anharmonicity depends on the kind of observable. The root mean square atomic fluctuations have significant anharmonic components at temperatures above 100 K. In contrast, the dihedral angle fluctuations are much closer to being harmonic at all the temperatures considered. The analysis of potentials of mean force experienced by individual atoms shows that atomic displacements have approximately Gaussian distributions from 50 to 300 K, with different force constants at each temperature (quasi-harmonic model). At 300 K, the force constants obtained by molecular dynamics are significantly lower than in the harmonic case. The time dependence of the projection of the molecular dynamics displacements on the normal mode coordinates shows that mode mixing is important above 100 K. The motions of the helix associated with the low-frequency normal modes are described and illustrated.

Synthesis, structure, and magnetism of the trinuclear copper(II) complex [Cu(CuL)2][ClO4]2[H2L = 3,3′-(trimethylenedinitrilo)bis(2-butanone oxime)]

Abstract: The trinuclear copper(II) complex [Cu(CuL)2][ClO4]2[H2L = 3,3′-(trimethylenedinitrilo)bis-(2-butanone oxime)] has been synthesized. It crystallizes in monoclinic space group C2/c, with Z= 4, a= 14.253(1), b= 18.798(2), c= 12.675(1)A, and β= 106.92(1)°. The structure consists of trinuclear cations [Cu(CuL)2]2+ and perchlorate ions. The central copper is co-ordinated by oximate oxygens of two CuL entities and the configuration around the metal is significantly distorted from tetrahedral with a dihedral angle of 33.31 (6)°. Each terminal copper adopts an essentially planar configuration with the nitrogen atoms of L2–. The three chromophores in the cation are bent at the edges of the bridging oximate oxygens, with a dihedral angle of 55.88(9)°, to afford a butterfly shape for the cation. In the crystal the trinuclear cations interact with each other at the terminal copper, in the so-called out-of-plane mode, through oximate oxygen to form an infinite chain along the c axis. Cryomagnetic investigations in the range 80–300 K revealed a strong antiferromagnetic spin-exchange interaction within the molecule; the magnetic moment per cation is 2.00 µB at room temperature but converges to 1.80 ± 0.01 µB at 170 K. The exchange integral J, based on the isotropic exchange model ℋ=–2∑jijŜiŜj, is –290.8 cm–1.

Conformational dependence of the one‐bond carbon–proton coupling constants in oligosaccharides

Abstract: A study is presented of the dependence on conformation of one-bond carbon-proton coupling constants in three 1-4-linked disaccharides. Calculated 1J(CH) values are based on the FPT formulation in the semi-empirical INDO MO method. The configuration at the anomeric carbon influences the 1J(CH) value, and the 1J(C-1′, H-1′) values are 20–30 Hz higher than the 1J(C-4, H-4) values. The conformational dependence of 1J(CH) on the dihedral angle about the CO bonds is satisfactorily expressed in the analytical form 1J(CH) = A cos 2ϕ + B cos ϕ. The constants A-E are different for the α- and β-anomers. Calculated average values 〈1J(C-1′, H-1′)〉 = 163.7 Hz and 〈1J(C-4, H-4)〉 = 146 Hz for methyl β-xylobioside using PCILO-calculated abundances of conformers agree well with the experimental values of 162.7 and 147.5 Hz, respectively.

A method for the analytic determination of polypeptide structure using solid state nuclear magnetic resonance: The ‘‘metric method’’

Abstract: A method, the metric method, is presented for determining the structure of polypeptides using solid state nuclear magnetic resonance (NMR) dipolar interactions. In analogy to the method of distance geometry used for protein structure determination from high resolution NMR spectroscopy, which is based on the general relationships that distances between points must satisfy, a method is developed here which makes use of the general relationships that angles between vectors must satisfy. With this method, analytical expressions are derived for the dihedral angles of the peptide backbone, and a way for minimizing the structural ambiguities associated with solid state NMR data is also presented. Calculations on a model polypeptide structure reveal the dipolar interactions of only the NH and NC1 bonds provide insufficient information for uniquely determining dihedral angles, even when constraints arising from long range interactions are employed, but these calculations yield a manageable number of solutions when...

Transition metal promoted reactions. 29. (Z)-2,2'-Disubstituted bifluorenylidenes by intramolecular desulfurdimerization reactions

Abstract: W(CO) 6 -mediated intramolecular desulfurdimerization reactions have been used in the syntheses of bridged 2,2'-disubstituted bifluorenylidenes in satisfactory yields. Ring sizes from 12 to 24 can be synthesized by this reaction. The extension of this reaction for the synthesis of bifluorenylidene-hinged crown ethers is described. The X-ray structure of 6i has been determined. The two fluorenylidene moieties are each planar, making a dihedral angle of 44.9°. The first optically active bifluorenylidenes were unequivocally synthesized, and the barriers for the racemization of two such molecules have been determined (12 kcal/mol)