Showing papers on "Dihedral angle published in 1989"

Three-dimensional solution structure of a single zinc finger DNA-binding domain.

Abstract: The three-dimensional solution structure of a zinc finger nucleic acid binding motif has been determined by nuclear magnetic resonance (NMR) spectroscopy. Spectra of a synthetic peptide corresponding to a single zinc finger from the Xenopus protein Xfin yielded distance and dihedral angle constraints that were used to generate structures from distance geometry and restrained molecular dynamics calculations. The zinc finger is an independently folded domain with a compact globular structure in which the zinc atom is bound by two cysteine and two histidine ligands. The polypeptide backbone fold consists of a well-defined helix, starting as alpha and ending as 3(10) helix, packed against two beta strands that are arranged in a hairpin structure. A high density of basic and polar amino acid side chains on the exposed face of the helix are probably involved in DNA binding.

Determination of the three-dimensional solution structure of the C-terminal domain of cellobiohydrolase I from Trichoderma reesei. A study using nuclear magnetic resonance and hybrid distance geometry-dynamical simulated annealing.

Abstract: The solution structure of a synthetic 36-residue polypeptide comprising the C-terminal cellulose binding domain of cellobiohydrolase I (CT-CBH I) from Trichoderma reesei was investigated by nuclear magnetic resonance (NMR) spectroscopy. The 1H NMR spectrum was completely assigned in a sequential manner by two-dimensional NMR techniques. A large number of stereospecific assignments for beta-methylene protons, as well as ranges for the phi, psi, and chi 1 torsion angles, were obtained on the basis of sequential and intraresidue nuclear Overhauser enhancement (NOE) and coupling constant data in combination with a conformational data base search. The structure calculations were carried out in an iterative manner by using the hybrid distance geometry-dynamical simulated annealing method. This involved computing a series of initial structures from a subset of the experimental data in order to resolve ambiguities in the assignments of some NOE cross-peaks arising from chemical shift degeneracy. Additionally, this permitted us to extend the stereospecific assignments to the alpha-methylene protons of glycine using information on phi torsion angles derived from the initial structure calculations. The final experimental data set consisted of 554 interproton distance restraints, 24 restraints for 12 hydrogen bonds, and 33 phi, 24 psi, and 25 chi 1 torsion angle restraints. CT-CBH I has two disulfide bridges whose pairing was previously unknown. Analysis of structures calculated with all three possible combinations of disulfide bonds, as well as without disulfide bonds, indicated that the correct disulfide bridge pairing was 8-25 and 19-35. Forty-one structures were computed with the 8-25 and 19-35 disulfide bridges, and the average atomic rms difference between the individual structures and the mean structure obtained by averaging their coordinates was 0.33 +/- 0.04 A for the backbone atoms and 0.52 +/- 0.06 A for all atoms. The protein has a wedgelike shape with an amphiphilic character, one face being predominantly hydrophilic and the other mainly hydrophobic. The principal element of secondary structure is made up of an irregular triple-stranded antiparallel beta-sheet composed of residues 5-9 (beta 1), 24-28 (beta 2), and 33-36 (beta 3) in which strand beta 3 is hydrogen bonded to the other two strands.(ABSTRACT TRUNCATED AT 400 WORDS)

Thermodynamics of Densification: I, Sintering of Simple Particle Arrays, Equilibrium Configurations, Pore Stability, and Shrinkage

Abstract: Equilibrium configurations for linear and closed arrays (rings and regular polyhedra containing a single pore) of identical particles (cylinders or spheres) were determined by minimizing the array's surface and grain-boundary energies with the assumption that each particle conserves its mass. The change in free energy between the initial and equilibrium configuration increases with dihedral angle (i.e., the equilibrium angle). More significantly, it is shown that pores will shrink to an equilibrium size if the number (n) of coordinating particles is greater than a critical value. The critical pore coordination number (nc) increases with the dihedral angle. Only pores with nnc are thermodynamically unstable during sintering. It is also shown that any mass-transport mechanism can lead to pore shrinkage while a connecting path to the pore surface remains open. The effective sintering “stress” (i.e., driving force) increases with the dihedral angle and decreases to zero as the equilibrium configuration is reached. Sintering stresses increase with decreasing coordination number. It is also shown that the shrinkage strain for closed arrays increases with the pore coordination number. Rearrangement phenomena within a powder compact are discussed with regard to resultant sintering forces on nonsymmetrically coordinated particles.

Preparation, structure, dynamics, and energetics of amorphous silicon: A molecular-dynamics study.

Abstract: The preparation of amorphous silicon by molecular-dynamics simulations employing the Stillinger-Weber Si potential, via direct slow cooling from the melt, is described. It is shown that previous failures to obtain amorphous Si using these interaction potentials are of kinetic origin, i.e., related to the quench rate employed. The amorphous silicon sample which we prepared exhibits structural and dynamical properties in good agreement with available experimental data for the static structure factor and phonon density of states. Detailed analyses of the structure, including distributions of bond and dihedral angles and ring statistics, and energetics, including the determination of effective temperatures for n-fold-coordinated atoms (n=3--5) and estimates of the formation energy of coordination defects (i.e., n\ensuremath{ e}4) are presented. The lack of medium-range order, measured via correlation between dihedral angles associated with adjacent bonds, is discussed.

Determination of the three-dimensional solution structure of the antihypertensive and antiviral protein BDS-I from the sea anemone Anemonia sulcata: a study using nuclear magnetic resonance and hybrid distance geometry-dynamical simulated annealing.

Abstract: The three-dimensional solution structure of the antihypertensive and antiviral protein BDS-I from the sea anemone Anemonia sulcata has been determined on the basis of 489 interproton and 24 hydrogen-bonding distance restraints supplemented by 23 {phi} backbone and 21 {sub {chi}1} side-chain torsion angle restraints derived from nuclear magnetic resonance (NMR) measurements. A total of 42 structures is calculated by a hybrid metric matrix distance geometry-dynamical simulated annealing approach. Both the backbone and side-chain atom positions are well defined. The average atomic rms difference between the 42 individual SA structures and the mean structure obtained by averaging their coordinates is 0.67 {plus minus} 0.12 {angstrom} for the backbone atoms and 0.90 {plus minus} 0.17 {angstrom} for all atoms. The core of the protein is formed by a triple-stranded antiparallel {beta}-sheet composed of residues 14-16 (strand 1), 30-34 (strand 2), and 37-41 (strand 3) with an additional mini-antiparallel {beta}-sheet at the N-terminus (residues 6-9). The first and second strands of the triple-stranded antiparallel {beta}-sheet are connected by a long exposed loop. A number of side-chain interactions are discussed in light of the structure.

The far infrared spectrum of H2O2. First observation of the staggering of the levels and determination of the cis barrier

Abstract: High resolution spectra of H2O2, recorded by means of Fourier transform spectroscopy between 30 and 460 cm−1, have been analyzed leading to the determination of the rotational levels of the torsional states (n,τ) for n=0,1,2,3. In order to reproduce these energy levels, Watson type Hamiltonians have been used and it has been possible to observe a staggering of the levels with n=2 and 3 caused by the cis barrier. The torsional band centers have then been fitted using a torsional Hamiltonian of the form {Bγγ,J2γ} +V(γ) with the potential function V(γ) written as V(γ)=V1 cos 2γ+V2 cos 4γ+V3 cos 6γ+V4 cos 8γ where the torsional coordinate 2γ is the dihedral angle defining the relative position of the two O–H bonds. The potential constants in cm−1 are V1=1036.97±23.1 cm−1, V2=657.53±5.2 cm−1, V3=50.89±3.3 cm−1, V4=2.524±0.83 cm−1 which correspond to barrier heights Vtrans =387.07±0.20 cm−1, Vcis =2562.8±60 cm−1, and to a potential minimum located at 2γ=111.9°±0.4° from the cis configuration. It is also shown t...

The possibility of molecular switching: Theoretical study of [(NH3)5Ru-4,4′-bipy-Ru(NH3)5]5+

Abstract: The possibility of molecular switching is investigated theoretically on a model system in which two redox active sites are connected by 4,4′-bipyridine. The electronic coupling between these sites is determined by two methods: the “dimer splitting” method and the effective Hamiltonian method. The pathways for electronic coupling are analyzed and computed for all dihedral angles between the pyridine cycles. It is found that the π-π coupling dominates the electronic interaction for most angle values. However, in strictly perpendicular conformation, the electronic interaction does not vanish, due to the existence of crossed σ-π interactions.

Interplay of Sintering Microstructures, Driving Forces, and Mass Transport Mechanisms

Abstract: The equilibrium shapes of segments of a row of sintering particles are calculated for the case where interparticle distances are constrained and, in particular, for only vapor-phase transport or surface diffusion active. These equilibrium states are contrasted with those obtained by mechanisms which allow densification. The sintering potentials and surface curvatures are calculated for the equilibrium shapes as a function of dihedral angle. Expressions for the rate of shrinkage are presented and, for the case of equilibrium structures, calculated exactly.

A solid state NMR study on crystalline forms of nylon 6

Abstract: High-resolution 13C-NMR spectra were studied for two different crystalline structures of nylon 6 in the solid state by the cross polarization/magic angle spinning (CP/MAS) method. Two crystalline structures, α-form and γ-form, gave different chemical shifts for methylene carbons. The results showed that the hydrogen bonds between intermolecular chains are stronger in the γ-form than in the α-form. This strongly supports the results of the X-ray study of nylon 6 by Malta et al. Our results also showed that interamolecular delocalization of positive charges occurs in the γ-form through hyperconjugation in which the dihedral angle between the π bond and neighboring σ bonds is 30° while no such effect can be expected in the α-form in which the angle is 0°.

Three-dimensional structure of the neurotoxin ATX Ia from Anemonia sulcata in aqueous solution determined by nuclear magnetic resonance spectroscopy.

Abstract: With the aid of 1H nuclear magnetic resonance (NMR) spectroscopy, the three-dimensional structure in aqueous solution was determined for ATX Ia, which is a 46 residue polypeptide neurotoxin of the sea anemone Anemonia sulcata. The input for the structure calculations consisted of 263 distance constraints from nuclear Overhauser effects (NOE) and 76 vicinal coupling constants. For the structure calculation several new or ammended programs were used in a revised strategy consisting of five successive computational steps. First, the program HABAS was used for a complete search of all backbone and chi 1 conformations that are compatible with the intraresidual and sequential NMR constraints. Second, using the program DISMAN, we extended this approach to pentapeptides by extensive sampling of all conformations that are consistent with the local and medium-range NMR constraints. Both steps resulted in the definition of additional dihedral angle constraints and in stereospecific assignments for a number of beta-methylene groups. In the next two steps DISMAN was used to obtain a group of eight conformers that contain no significant residual violations of the NMR constraints or van der Waals contacts. Finally, these structures were subjected to restrained energy refinement with a modified version of the molecular mechanics module of AMBER, which in addition to the energy force field includes potentials for the NOE distance constraints and the dihedral angle constraints. The average of the pairwise minimal RMS distances between the resulting refined conformers calculated for the well defined molecular core, which contains the backbone atoms of 35 residues and 20 interior side chains, is 1.5 +/- 0.3 A. This core is formed by a four-stranded beta-sheet connected by two well-defined loops, and there is an additional flexible loop consisting of the eleven residues 8-18. The core of the protein is stabilized by three disulfide bridges, which are surrounded by hydrophobic residues and shielded on one side by hydrophilic residues.

Three-dimensional solution structure of a DNA duplex containing the BclI restriction sequence: two-dimensional NMR studies, distance geometry calculations, and refinement by back-calculation of the NOESY spectrum.

Abstract: A three-dimensional solution structure for the self-complementary dodecanucleotide [d-(GCCTGATCAGGC)]2 has been determined by distance geometry with further refinements being performed after back-calculation of the NOESY spectrum. This DNA dodecamer contains the hexamer [d(TGATCA)]2 recognized and cut by the restriction endonuclease BclI, and its structure was determined in hopes of obtaining a better understanding of the sequence-specific interactions which occur between proteins and DNA. Preliminary examination of the structure indicates the structure is underwound with respect to idealized B-form DNA though some of the local structural parameters (glycosyl torsion angle and pseudorotation angle) suggest a B-family type of structure is present. This research demonstrates the requirements (resonance assignments, interproton distance measurements, distance geometry calculations, and NOESY spectra back-calculation) to generate experimentally self-consistent solution structures for short DNA sequences.

Reaction path study of conformational transitions and helix formation in a tetrapeptide

Abstract: Conformational transitions between the 112 stable states of the tetrapeptide isobutyryl-Ala3-NH-methyl (IAN) are studied theoretically. The objective of the investigation is to advance the understanding of helix formation and of conformational transitions in polypeptides. The possible reaction paths between extended chain and helical configurations are examined in detail. The study of the multiple reaction paths in this 48-atom molecule became possible due to development of a new computational algorithm. It is shown that the helix-coil transitions in IAN follow a sequence of local dihedral flips and that the number of the available routes for the transition is significantly lower than in a random search. A quasi-melting point is obtained at 5 +/- 1 kcal (1 cal = 4.18 J)/mol above the lowest energy minimum. Below this point the molecule is trapped in one or very few minima, and above it the molecule hops between a large number of configurations.

The importance of the orientation of the C9 substituent to cannabinoid activity.

Abstract: We have found a correlation between cannabinoid psychopharmacological activity and the orientation of the C9 substituent in one class of cannabinoid derivatives. We report here a study of the active cannabinoids delta 9-tetra-hydrocannabinol (delta 9-THC), delta 8-tetrahydrocannabinol (delta 8-THC), and 11 beta-hexahydrocannabinol (11 beta-HHC); the minimally active cannabinoid 11 alpha-hexahydrocannabinol (11 alpha-HHC); and the inactive cannabinoids delta 7-tetrahydrocannabinol (delta 7-THC) and delta 9,11-tetrahydrocannabinol (delta 9,11-THC). Our working hypothesis is that there are two components of cannabinoid structure which confer upon these compounds reactivity characteristics crucial to activity: the directionality of the lone pairs of electrons of the phenyl group hydroxyl oxygen and the orientation of the carbocyclic ring relative to this oxygen. The structures of these six molecules were optimized by using the method of molecular mechanics as encoded in the MMP2(85) program. Other possible minimum-energy conformations of the carbocyclic ring were calculated by driving one torsion angle in this ring by use of the dihedral driver option in MMP2(85). The rotational energy behavior of the phenyl group hydroxyl in each molecule was studied also by using the dihedral driver option in MMP2(85). We found that the carbocyclic ring in 11 alpha-HHC can exist in either a chair or a twist conformation. The carbocyclic ring in delta 9-THC, in delta 8-THC, and in delta 7-THC was found to exist only in a half-chair conformation, while the carbocyclic ring in 11 beta-HHC and in delta 9,11-THC was found to exist only in a chair form. The results of the rotational energy profiles indicated that the minimum-energy positions of the phenyl group hydroxyls are nearly identical in all molecules. These molecules, then, were found to differ only in the conformation of the carbocyclic ring in each. This conformation, in turn, determines the orientation of this ring and its C9 substituent relative to the oxygen of the phenyl group hydroxyl. In order to assess the orientation of the carbocyclic ring with respect to the phenyl group hydroxyl oxygen in each optimized structure, the following nonbonded torsion angles were measured: C10-C10a-C1-O, C8-C7-C1-O, C11-C9-C1-O, and C9-Q-C1-O (where Q is a dummy atom placed midway between C8 and C10).(ABSTRACT TRUNCATED AT 400 WORDS)

Direct measurements of energy transfer between identical chromophores in solution

Abstract: The rate of intramolecular electronic excitation energy transfer in 9,9’ bifluorene has been investigated in a variety of solvents, using both time‐correlated single photon counting and femtosecond fluorescence upconversion technique. The kinetics of energy transfer were determined in both cases by time dependent fluorescence anisotropy measurements. The energy transfer dynamics between fluorene moieties has been found to occur on a time scale of approximately 600 fs in different solvents and has been correlated with the T2 value calculated from the absorption linewidth and the β value obtained from jet measurements. The dihedral angle between the fluorene moieties was also calculated from the anisotropy measurement and compared with the values obtained from a solution phase NMR determination.

Conformational analysis and molecular modeling of 1-phenyl-, 4-phenyl-, and 1-benzyl-1,2,3,4-tetrahydroisoquinolines as D1 dopamine receptor ligands

Abstract: Conformational studies on a series of 1-phenyl-, 4-phenyl-, and 1-benzyl-1,2,3,4-tetrahydroisoquinolines that possess an identical substituent pattern to the prototypical D1 dopamine receptor antagonist SCH23390 [(R)-(+)-7-chloro-8-hydroxy-3-methyl-1-phenyl-2,3,4,5- tetrahydro-1H-3-benzazepine (1)] were performed with use of molecular mechanics calculations [MM2(85), with newly developed aromatic halide bending and torsional parameters that are now incorporated into MM2(87)], single-crystal X-ray analysis, and high-field NMR spectroscopy. The synthesis and biological testing of compounds 2-7 has been previously reported. The test compounds were compared both quantitatively and graphically to compound 1. Calculations on both the free-base and protonated forms of each compound were carried out. To insure that conformation space was adequately sampled, the test compounds were energy minimized from different starting geometries; ring inversion of the heterocycle was employed, as were dihedral driver calculations on the phenyl or benzyl rings. For N-methyl-6-chloro-7-hydroxy-1-phenyl-1,2,3,4-tetrahydroisoquinoline (2), it was determined that the torsion angle tau(C8a-C1-C12-C17) had energy minima at approximately 60 degrees and 240 degrees. This finding was corroborated by NMR studies that indicated a dramatic upfield chemical shift of ArH8 after ring cyclization. The nitrogen lone pair or hydrogen vector was approximately orthogonal to the plane of the substituted aromatic ring in the tetrahydroisoquinolines; this explained the upfield chemical shift of the vicinal chiral proton (H1). In all instances, the 6-membered heterocyclic ring in the energy-minimized structures preferred the half-chair conformation with the phenyl rings pseudo-equatorial. Distance comparisons of the proposed pharmacophoric atoms (Cl, N, O, centroid of the phenyl or benzyl ring) showed that the phenyl or benzyl centroid to ammonium H distance, Cl to N distance, and distance of the nitrogen above or below the plane of the isoquinoline aromatic ring are the distances most highly correlated with biological activity (r = 0.82, 0.75, 0.81, respectively). Resolution and single-crystal X-ray analysis of compound 2 showed the most active enantiomer to possess the S absolute configuration, in contrast to the benzazepine (R)-1. Least-squares fitting of the energy-minimized structures with SYBYL molecular modeling software showed (S)-(+)-2, rather than (R)-(-)-2, gave a better fit to (R)-1. Volume determinations derived from SYBYL multifit analyses aided in receptor mapping to qualitatively describe areas of "active" pharmacophore space as well as areas of "inactive" substituent space.(ABSTRACT TRUNCATED AT 400 WORDS)

A theoretical model of phospholipid dynamics in membranes

Abstract: Static and dynamic properties related to the internal configurational motions have been calculated for the alkyl chains of phospholipid molecules in a membrane environment in the liquid crystal phase The calculations have been performed for the chain 1 of 1,2‐dipalmitoyl 3‐sn‐phosphatidylcholine (DPPC), a typical constituent of phospholipid membranes Under the assumption of fixed bond lengths and bond angles, the internal dynamics of the chain is described in terms of 15 dihedral angles The time evolution of the angular variables is assumed to be diffusional in character, and a master equation for transitions among the stable conformers is constructed from the energetics and hydrodynamics of the chain This method is an extension to the time domain of the rotational isomeric state (RIS) approximation, which has been widely used to compute static properties of the chains After calculation of the suitable correlation functions, effective rate constants relevant for spectroscopic and kinetic observables have been computed, and the results have been compared with those obtained by recent Brownian dynamics (BD) calculations The position dependence of the rate constants along the chain has been examined with special reference to understanding the effects resulting from cooperativity in the conformational transitions The overall spinning and tumbling of the chain has also been described by a diffusive model The calculated spectral densities for the composite motional process have been used to rationalize the behavior of the relaxation times T1, T2, and T1ρ measured in deuterium nuclear magnetic resonance (NMR) experiments

Solution structures of proteins from NMR data and modeling: Alternative folds for neutrophil peptide 5

Abstract: The structure of neutrophil peptide 5 in solution has recently been reported (Pardi et al., 1988). The structure determination was accomplished by using a distance geometry algorithm and 107 interproton distance constraints obtained from 2D NMR data. In each of the eight independent solutions to the distance geometry equations, the overall fold of the polypeptide backbone was identical and the root mean square (rms) deviation between backbone atoms of the superimposed structures was small (approximately 2.4 A). In this paper we report additional NP-5 structures obtained by using a new structure generation algorithm: a Monte Carlo search in torsion angle space. These structures have a large rms backbone deviation from the distance geometry structures (approximately 5.0 A). The backbone topologies differ in significant respects from the distance geometry structures and from each other. Structures are found that are pseudo mirror images of part or all of the fold corresponding to that first obtained with the distance geometry procedure. For small proteins, the problem of distinguishing the correct structure among pseudo mirror images is likely to be greater than previously recognized. When a set of test distance constraints constructed from a novel Monte Carlo structure is used as input in the distance geometry algorithm, the fold of the resulting structure does not correspond to that of the target. The results also demonstrate that the previously accepted criteria (the magnitude of the rms deviation between multiple solutions of the distance geometry equations) for defining the accuracy and precision of a peptide structure generated from NMR data are inadequate. An energetic analysis of structures corresponding to the different folding topologies has been carried out. The molecular mechanics energies obtained by minimization and molecular dynamics refinement provide sufficient information to eliminate certain alternative structures. On the basis of a careful comparison of the different trial structures with the experimental data, it is concluded that the NP-5 peptide fold which was originally reported is most consistent with the data. An alternative fold corresponding to structures with low energies and small total distance violations is ruled out because for this fold predicted NOEs are not observed experimentally.

Remarks on the barrier to rotation about the Csp2—O bond in anisole

Abstract: Molecular orbital computations with the basis set 6-31G are reported for seven values of θ, the torsion angle about the bond in anisole. All bond angles and lengths are optimized but the atoms of t...

Conformational stability, barriers to internal rotation, vibrational assignment, and ab initio calculations of chloroacetyl fluoride

Abstract: The far infrared spectrum of gaseous chloroacetyl fluoride, CH2ClC(O)F, has been recorded at a resolution of 0.10 cm−1 in the 350 to 35 cm−1 region. The fundamental asymmetric torsional frequencies of the more stable trans (two halogen atoms oriented trans to one another) and high energy gauche (Cl–C–C=O torsional dihedral angle of 122°) have been observed at 86.5 and 48.8 cm−1, respectively, each with excited states falling to lower frequency. From these data the asymmetric torsional potential function governing internal rotation about the C–C bond has been determined. This potential function is consistent with torsional potential coefficients of: V1=350±12, V2=306±6, V3=420±1, V4=44±1, and V6=2±1 cm−1. The trans to gauche, gauche to gauche, and gauche to trans barriers have been determined to be 796, 245, and 271 cm−1, respectively, with an energy difference between the conformations of 525±24 cm−1 (1.50±0.07 kcal/mol). From studies of the Raman spectrum at variable temperatures the conformational energ...

RCS analysis and reduction for lossy dihedral corner reflectors

Abstract: The radar cross-section patterns of lossy dihedral corner reflectors are calculated using a uniform geometrical theory of diffraction for impedance surfaces All terms of up to third order reflections and diffractions are considered for patterns in the principal plane The surface waves are included whenever they exist for reactive surface impedances The dihedral corner reflectors examined have right, obtuse, and acute interior angles, and patterns over the entire 360 degrees azimuthal plane are calculated The surface impedances can be different on the four faces of the dihedral corner reflector; however, the surface impedance must be uniform over each face Computed cross sections are compared with a moment method technique for a dielectric/ferrite absorber coating on a metallic corner reflector The analysis of the dihedral corner reflector is important because it demonstrates many of the important scattering contributors of complex targets including both interior and exterior wedge diffraction, half-plane diffraction, and dominant multiple reflections and diffractions >

The shapes of first‐stage sinters

Abstract: The shape of first‐stage sinters is derived within a framework in which a solid skeleton is wetted by a mobile‘‘liquid’’ pool. Several lattices are considered as possible solid skeletons, corresponding to various degrees of surface versus grain boundary and volume transport; the effect of a nonzero dihedral angle at the interface between crystal faces is also treated. In some cases, significant differences exist between shapes calculated by minimizing the free energy and the shapes assumed by previous workers.

Structural, spectroscopic and theoretical studies of novel d6 fac-bromotricarbonyl(dithiooxamide)rhenium complexes

Abstract: This article describes the syntheses and X-ray structures of three novel complexes Re(CO) 3 (DTO)Br which differ in the dihedral angle between the thioamide groups of their DTO ligands. The structural data have been used for LCAO−Xα MO calculations on the model complex Re(CO) 3 (H 2 -DTO)Br. Major differences in the structures and electronic absorption spectra are interpreted with the use of MO diagrams, orbital contour plots, calculated electronic interactions, and steric properties of the complexes

Theoretical study of conformations of some heterocyclic transition-metal complexes

Abstract: The conformations for heterocyclic transition-metal sandwich complexes involving five-membered rings (C 4 H 4 X 2 )M with X=P, As, and Sb, six-membered rings such as (C 5 H 6 B) 2 M and (C 5 H 5 N) 2 M, and some five-membered polyheterocyclic rings are studied by use of the extended Huckel method. The calculations are in good agreement with the observed results. The main purpose of this work is to identify the key orbitals for the observed dihedral angles. The general pattern emerging from this study is that the metal (D xz , d yz ) pair favors 90˚ conformation, for it allows them to interact independently with ring orbitals

Quantification of DNA structure from NMR data: conformation of d-ACATCGATGT.

Abstract: Resonance assignments of nonexchangeable base and sugar protons have been obtained in double-helical d-ACATCGATGT by using two-dimensional correlated spectroscopy (COSY) and nuclear Overhauser enhancement spectroscopy (NOESY). The exchangeable imino protons have been assigned on the basis of their chemical shifts. The characteristic phase-sensitive multiplet patterns of the intrasugar cross-peaks in the omega 1-scaled COSY spectrum have been used to estimate several scalar coupling constants (J). The information on the J values combined with the intranucleotide COSY cross-peak intensities has been used to identify sugar puckers of individual nucleotide units. In most cases, the deoxyribofuranose rings are found to adopt a conformation close to O4'-endo. Spin diffusion has been monitored from the buildup of the normalized volumes of NOE cross-peaks in NOESY spectra as a function of mixing time. A set of 52 intranucleotide and internucleotide proton-proton distances have been estimated by using low mixing time NOESY spectra (tau m = 40 and 80 ms). The estimated intrasugar proton-proton distances rule out possibilities of existence of a fast equilibrium between C2'-endo and C3'-endo conformations. Intranucleotide proton-proton distances combined with the knowledge of sugar puckers have been used to fix the glycosidic bond torsion angle (chi). For this purpose, simulated distance contours depicting the dependence of intranucleotide proton-proton distances on pseudorotational phase angle (P) and glycosidic bond torsion angle (chi) have been used. Further, the proton homonuclear (J, delta) spectrum has been used to monitor the 31P-1H heteronuclear couplings, which are preserved in the omega 2 projection.(ABSTRACT TRUNCATED AT 250 WORDS)