Dihedral angle study in Hesperidin using NMR Spectroscopy

Hesperidin is flavonoid molecule found in citrus fruits (Citrus reticulata), especially difficult to extract, classify and characterize. Present work is to study the unresolved relative configuration of Hesperidin through the dihedral angle, coupling constant and different NMR techniques. The Karplus equation and its modifications have been originated from the valence bond theory and associated with dihedral angle and coupling constant. The result data set of calculated dihedral angle can probe significant method to assign the virtual configuration of natural products and also resolved stereochemistry of Hesperidin at C‐2 position in. Copyright © 2016 John Wiley & Sons, Ltd.     

Force-field parametrization of retro-inverso modified residues: Development of torsional and electrostatic parameters

Summary Torsional and the electrostatic parameters for molecular mechanics studies of retro-inverso modified peptides have been developed using quantum mechanical calculations. The resulting parameters have been compared with those calculated for conventional peptides. Rotational profiles, which were obtained spanning the corresponding dihedral angle, were corrected by removing the energy contributions associated to changes in interactions different from torsion under study. For this purpose, the torsional energy associated to each point of the profiles was estimated as the corresponding quantum mechanical energy minus the bonding and nonbonding energy contributions produced by the perturbations that the variation of the spanned dihedral angle causes in the bond distances, bond angles and the other dihedral angles. These energies were calculated using force-field expressions. The corrected profiles were fitted to a three-term Fourier expansion to derive the torsional parameters. Atomic charges for retro-inverso modified residues were derived from the rigorously calculated quantum mechanical electrostatic potential. Furthermore, the reliability of electrostatic models based on geometry-dependent charges and fixed charges has been examined.     

Theoretical study of building blocks for molecular switches based on electrically induced conformational changes

We present an investigation of building blocks for molecular torsional switches made up of two distinct aromatic moieties, possibly bonded through one or more acetynil groups. The mechanism of operation is based on the action of a static electric field perpendicular to the ring–ring bond, which can modulate the torsional angle and, as a consequence, the inter-ring conjugation. The action of the perpendicular electric field on the dihedral angle is shown to increase, as a result of the inclusion of suitable substituents on the aromatic rings. By computing the response of the electron density of a molecule, with an excess electron, to a longitudinal electric field, we show that the intramolecular electron transfer is sensitive to the torsional angle. This feature can be conveniently rationalized in terms of a potential barrier which is created along the molecule as the dihedral angle varies from the co-planar to the perpendicular position.     

An ab initio MO study on the disulfide bond: properties concerning the characteristic S-S dihedral angle

The characteristics of disulfide groups concerning the S-S dihedral angle are represented by ab initio SCF calculations using the split-valence 6-31G(^*) basis set. It is shown that the hyperconjugation between the S-H bond and the electron pair on the other sulfur plays an important role in determining the characteristic S-S dihedral angle. The S 3d orbitals do not participate in such characteristics. The nature of the S-S bond is compared with that of the O-O bond. The S-S bond length varies largely depending on the S-S dihedral angle. This is related to the frequency-conformation correlation of the disulfide group.     

Gauche effect in 1,2-difluoroethane. Hyperconjugation, bent bonds, steric repulsion

Natural bond orbital deletion calculations show that whereas the gauche preference arises from vicinal hyperconjugative interaction between anti C-H bonds and C-F* antibonds, the cis C-H/C-F* interactions are substantial (approximately 25% of the anti interaction). The established significantly >60 degrees FCCF dihedral angle for the equilibrium conformer can then be rationalized in terms of the hyperconjugation model alone by taking into account both anti interactions that maximize near 60 degrees and the smaller cis interactions that maximize at a much larger dihedral angle. This explanation does not invoke repulsive forces to rationalize the 72 degrees equilibrium conformer angle. The relative minimum energy for the trans conformer is the consequence of a balance between decreasing hyperconjugative stabilization and decreasing steric destabilization as the FCCF torsional angle approaches 180 degrees . The torsional coordinate is predicted to be strongly contaminated by CCF bending, with the result that approximately half of the trans --> gauche stabilization energy stems from mode coupling.     

Correlation of dihedral angles with 13C chemical shifts of quaternary carbon atoms of some phenothiazine derivatives

A direct relationship between the ¹³C nmr chemical shifts of the quaternary carbon atoms of the central ring of phenothiazine and the dihedral angle of the respective derivatives has been observed. This correlation allows for the useful and quick estimation of the dihedral angles of novel phenothiazines from readily obtainable ¹³C nmr solution measurements. In addition, the change in the dihedral angle appears to be directly related to the S-C_4a-C_10a bond angle; however, the C_4a-S-C_5a bond angle is not affected by changes in the dihedral angle. This indicates that the “flattening” of the phenothiazine tricyclic ring system is compensated for by the vertical displacement of the sulfur atom, by changes in hybridization of N₁₀, and by other angular distortions of the middle ring.     

An apparent angle dependence for the nonradiative deactivation of excited triplet states of sterically constrained, binuclear ruthenium(II) bis(2,2':6',2' '-terpyridine) complexes

The photophysical properties are reported for a series of binuclear ruthenium(II) bis(2,2':6',2"-terpyridine) complexes built around a geometrically constrained, biphenyl-based bridge. The luminescence quantum yield and lifetime increase progressively with decreasing temperature, but the derived rate constant for nonradiative decay of the lowest-energy triplet state depends on the length of a tethering strap attached at the 2,2'-positions of the biphenyl unit. Since the length of the strap determines the dihedral angle for the central C-C bond, the rate of nonradiative decay shows a pronounced dependence on angle. The minimum rate of nonradiative decay occurs when the dihedral angle is 90 degrees, but there is a maximum in the rate when the dihedral angle is about 45 degrees. This effect does not appear to be related to the extent of electron delocalization at the triplet level but can be explained in terms of variable coupling with a low-frequency vibrational mode associated with the strapped biphenyl unit.     

Conformational analysis of furanose rings with PSEUROT: parametrization for rings possessing the arabino,lyxo, ribo,and xylo stereochemistry and application to arabinofuranosides

The solution conformation of a furanose ring can be assessed through PSEUROT analysis of three-bond (1)H-(1)H coupling constants ((3)J(HH)) of the ring hydrogens. For each coupling constant, PSEUROT requires two parameters, A and B, which are used to translate the H[bond]C[bond]C[bond]H dihedral angle predicted from the (3)J(HH) into an endocyclic torsion angle from which the identity of the conformers can be determined. In this paper, we have used density functional theory methods to generate a family of envelope conformers for methyl furanosides 1-8. From these structures, A and B were calculated for each H[bond]C[bond]C[bond]H fragment. In turn, the values of these parameters for the arabinofuranose ring were used in PSEUROT calculations to determine the conformers populated by monosaccharides 1 and 2 as well as the furanose rings in oligosaccharides 9-15. The results of these analyses are consistent with the low-energy conformers identified from previous computational and X-ray crystallographic studies of 1 and 2.     

非晶硅短程序与电子结构关系的量子化学研究

本支通过对Si_(29)无规网络原子簇模型的CNDO计算,探讨了非晶硅(a-Si)结构短程序对其电子态密度(DOS)分布的影响。结果表明,在与实验原子径向分布函数(RDF)基本相同的条件下,a-Si模型中的键角和二面角是影响电子态密度分布的主要参数。     

Conformational memories with variable bond angles

Conformational Memories (CM) is a simulated annealing/Monte Carlo method that explores peptide and protein dihedral conformational space completely and efficiently, independent of the original conformation. Here we extend the CM method to include the variation of a randomly chosen bond angle, in addition to the standard variation of two or three randomly chosen dihedral angles, in each Monte Carlo trial of the CM exploratory and biased phases. We test the hypothesis that the inclusion of variable bond angles in CM leads to an improved sampling of conformational space. We compare the results with variable bond angles to CM with no bond angle variation for the following systems: (1) the pentapeptide Met-enkephalin, which is a standard test case for conformational search methods; (2) the proline ring pucker in a 17mer model peptide, (Ala)(8)Pro(Ala)(8); and (3) the conformations of the Ser 7.39 chi(1) in transmembrane helix 7 (TMH7) of the cannabinoid CB1 receptor, a 25-residue system. In each case, analysis of the CM results shows that the inclusion of variable bond angles results in sampling of regions of conformational space that are inaccessible to CM calculations with only variable dihedral angles, and/or a shift in conformational populations from those calculated when variable bond angles are not included. The incorporation of variable bond angles leads to an improved sampling of conformational space without loss of efficiency. Our examples show that this improved sampling leads to better exploration of biologically relevant conformations that have been experimentally validated.     

A harmonic oscillator model of the conformationally flexible helical polymeric molecules

The approach of the persistence vector to its asymptotic limit can be characterized by the average projection of a unit vector along the last bond onto a unit vector along the first bond. The behavior of this projection has been examined in simple, predominantly helical chains in which limited flexibility is introduced by either of two devices: occurrence in an average way of a configuration much different from that required for helix propagation, and use of a square-well potential centered at the dihedral angle utilized in a rigid helix. The manner in which flexibility is introduced determines the behavior of the angular frequency as well as the relative decay rates for oscillations and the midpoint about which oscillations occur.     

Polysulfide anions II: structure and vibrational spectra of the S4(2-) and S5(2-) anions. Influence of the cations on bond length, valence, and torsion angle

The influence of the cations on bond length, valence, and torsion angle of S4(2-) and S5(2-) anions was examined in a series of solid alkali tetra- and pentasulfides by relating their Raman spectra to their known X-ray structures through a force-field analysis. The IR and Raman spectra of BaS4.H2O and the Raman spectra of (NH4)2S4.nNH3, gamma-Na2S4, and delta-Na2S5 are presented. The similarity of spectra of gamma-Na2S4 with those of BaS4.H2O suggests similar structures of the S4(2-) anions in these two compounds with a torsion angle smaller than 90 degrees. The variations of SS bond length, SSS valence angle, and dihedral angle of Sn2- anions are related to the polarization of the lone pair and electronic charge of the anion by the electric field of the cations. A correlation between the torsion angle and the SSS valence angle is shown as that previously reported between the length of the bond around which the torsion takes place and the dihedral angle value. These geometry changes are explained by the hyperconjugation concept and the electron long-pair repulsion.     

Cyclic peroxides: dihedral angle around the peroxide bond by microwave and photoelectron spectroscopic studies

Experimental COOC dihedral angles are used to support the relation proposed by Coughlin et al. for correlating the observed photoelectron splitting n(O)⁺- with the dihedral angle around the peroxide bond in cyclic peroxides.     

Comparative study on the transition structures of (3,4) and (3,5) ene cyclizations: A theoretical approach

Possible transition structures (TSs) of (3,4) and (3,5) ene cyclizations of 7-methyl-1,6-octadiene and 7-methylocta-1,6-dien-3-one were constructed and optimized by DFT method. Product proportions were calculated using the relative energies of the transition structures and these results are found to be in good agreement with the experimental one. Variation of the product proportions was explained using some model TSs of intermolecular ene reactions. The change of the dihedral angle around the forming carbon–carbon bond in the model transition structures was found to play a crucial role in determining the overall selectivities of cyclized products.     

Using operators to expand the block matrices forming the Hessian of a molecular potential

We derive compact expressions of the second‐order derivatives of bond length, bond angle, and proper and improper torsion angle potentials, in terms of operators represented in two orthonormal bases. Hereby, simple rules to generate the Hessian of an internal coordinate or a molecular potential can be formulated. The algorithms we provide can be implemented efficiently in high‐level programming languages using vectorization. Finally, the method leads to compact expressions for a second‐order expansion of an internal coordinate or a molecular potential. © 2014 Wiley Periodicals, Inc.     

Theoretical study of nucleophilic substitution at the disulfide bridge of cyclo-l-cystine

The reaction of cyclo-l-cystine with thiolate is examined at the B3LYP/6-31+G level. The two isomers of cyclo-l-cystine differ in their dihedral angle about the disulfide bond; the M isomer (with dihedral angle of -90.1 degrees) is found to be slightly lower in energy. The nucleophilic substitution reaction at sulfur follows the addition-elimination mechanism, exemplified by the hypercoordinate sulfur intermediate on the reaction surface. The reaction is exergonic (DeltaG = -6.16 kcal mol(-1)), and both the entrance and exit transition state lie below the reactant energies.     

Trifluoromethyl chlorosulfonate, CF3OSO2Cl: gas phase and crystal structure, conformation and vibrational analysis studied by experimental and theoretical methods

The geometric structure and conformational properties of trifluoromethyl chlorosulfonate (chlorosulfuric acid trifluoromethyl ester), CF(3)OSO(2)Cl, have been determined by X-ray crystallography, gas electron diffraction (GED), and vibrational spectroscopy (IR(gas), IR(matrix), and Raman(liquid)). These experimental investigations were supplemented by quantum chemical calculations (B3LYP with 6-311G* and 6-311+G(3df) basis sets). All experimental methods result in a single conformer with gauche orientation of the CF(3) group relative to the S[bond]Cl. The dihedral angle delta(COSCl) is determined to be 91.7(3) degrees in the crystal and 94(3) degrees in the gas phase. This dihedral angle corresponds to a near-eclipsed orientation of the O[bond]C relative to one of the S[double bond]O bonds (delta(CO[bond]SO) = -23.0(3) degrees and -21(3) degrees in the crystal and gas phase, respectively).     

A microwave spectroscopic and quantum chemical study of propa-1,2-dienyl selenocyanate (H(2)==C==CHSeC[triple bond]N) and cyclopropyl selenocyanate (C(3)H(5)SeC[triple bond]N)

The microwave spectra of propa-1,2-dienyl selenocyanate, H(2)C==C==CHSeC[triple bond]N, and cyclopropyl selenocyanate, C(3)H(5)SeC[triple bond]N, are reported. The spectra of the ground and two vibrationally excited states of the (80)Se isotopologue and the spectrum of the ground state of the (78)Se isotopologue were assigned for one rotameric form of H(2)C==C[double bond, length as m-dash]CHSeC[triple bond]N. This conformer is characterized by a C-C-Se-C dihedral angle of 129(5) degrees from synperiplanar (0 degrees ) and is shown to be the global minimum of H(2)C[double bond, length as m-dash]C[double bond, length as m-dash]CHSeC[triple bond]N. The spectra of the ground and of three vibrationally excited states of the (80)Se isotopologue, as well as of the ground state of the (78)Se isotopologue of one rotamer of C(3)H(5)SeC[triple bond]N were assigned. This conformer has a H-C-Se-C dihedral angle of 80(4) degrees from synperiplanar and is at least 3 kJ mol(-1) more stable than any other form of the molecule. The microwave study has been augmented by quantum chemical calculations at the B3LYP/6-311+ +G(3df,3pd) and MP2/6-311+ +G(3df,3pd) levels of theory.     

Bond length distortions associated with torsion potentials; ab-initio studies on methanediol

The 4-31G basis set is used to study the bond length variations as functions of dihedral angels in methanediol. This study is compared with OCO bond angle optimization studies by Gorenstein and Kar and the possible reason for bond length shorteing in the transtrans configuration is analysed.