Home About us Contact
|
Home About us Contact | ||
|
|
||
Torsional Angles (torsional + angle)
Selected AbstractsHydrodynamic modeling of diffusion tensor properties of flexible moleculesJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 1 2009Vincenzo Barone Abstract We present a computationally efficient implementation of hydrodynamic modeling for the evaluation of diffusion tensors of molecules with internal degrees of freedom, adapted to take into account information from linear scaling computations of solvent accessible surfaces implemented in the framework of last generation continuum solvent models. Torsional angles are taken also explicitly into account, while retaining correct hydrodynamic interactions. A comparison with literature data is presented to prove the effectiveness of the approach for a wide range of molecular dimensions and solvent environments. © 2008 Wiley Periodicals, Inc. J Comput Chem, 2009 [source] Shake table tests on a mass eccentric model with base isolationEARTHQUAKE ENGINEERING AND STRUCTURAL DYNAMICS, Issue 9 2003Bijan Samali Abstract A mass eccentric structure is usually more seismically vulnerable than its concentric counterpart because of the coupled torsional,translational response of such structures. In this work, dynamic characteristics and response of a five-storey benchmark model with moderate mass eccentricity were investigated using a shake table, simulating four different ground motions. The effectiveness of laminated rubber bearings (LRB) and lead-core rubber bearings (LCRB) in protecting eccentric structures was examined and evaluated in relation to translational and torsional responses of the benchmark model. It was observed that both translational and torsional responses were significantly reduced with the addition of either a LRB or LCRB isolated system regardless of the nature of ground motion input. The LRB were identified to be more effective than LCRB in reducing model relative displacements, the relative torsional angle as well as accelerations, and therefore provided a better protection of the superstructure and its contents. On the other hand, LCRB rendered a smaller torsional angle and absolute displacement of the base isolation system, hence a more stable structural system. Copyright © 2003 John Wiley & Sons, Ltd. [source] Ultralong Carbon,Carbon Bonds in Dispirobis(10-methylacridan) Derivatives with an Acenaphthene, Pyracene, or Dihydropyracylene SkeletonCHEMISTRY - A EUROPEAN JOURNAL, Issue 19 2008Hidetoshi Kawai Dr. Abstract Acenapthalene, pyracene, and dihydropyracylene attached to two units of spiroacridan are a novel class of hexaphenylethane (HPE) derivatives that have an ultralong CC bond (1.77,1.70,Å). These sterically challenged molecules were cleanly prepared by CC bond formation through two-electron reduction from the less-hindered dications. These ultralong bonds were realized based on several molecular-design concepts including enhanced "front strain" through "multiclamping" by means of fusing or bridging aryl groups in the HPE molecule. The lengths of these ultralong bonds and their relation to the conformation (torsional angle) were also validated by means of theoretical calculations. Bond-fission experiments revealed that the bonds are more easily cleaved than standard covalent bonds to produce the corresponding dication upon oxidation with an increase in the length of the CC bond. [source] Circular dichroism of diglycosyl dichalcogenides in solution and solid state,CHIRALITY, Issue 3-4 2008Tibor Kurtán Abstract Solution and solid-state CD spectra of nine peracetylated and deacetalyted diglycosyl disulfides were measured to study the relationship between the low-energy CD transitions (n1,,*SS and n2,,*SS) and helicity of the inherently chiral disulfide chromophore as perturbed by chiral carbohydrate moieties. The solid-state CD spectra were directly correlated with the reported X-ray structures of Ac4GlcSSGlcAc4 and Ac4GlcSSGalAc4, and the CD data revealed that all the disulfides have M helicity with C1SSC1, dihedral angles ,90° < , < 0° both in solution and in the solid state. A TDDFT CD study was carried out on dimethyl diselenide which confirmed that the same quadrant rule is relevant between the signs of the low-energy CD transitions and the diselenide torsional angle as formulated previously for the disulfide chromophore. The CD spectra of Ac4GlcSeSeGlcAc4 measured in solution and in the solid state were correlated with its X-ray structure and reproduced well by TDDFT CD calculations performed on its tetra- O -acetyl derivative. Chirality, 2008. © 2007 Wiley-Liss, Inc. [source] Conformational studies on a unique bis-sulfated glycolipid using NMR spectroscopy and molecular dynamics simulationsFEBS JOURNAL, Issue 23 2000Naoko Iida-Tanaka The time-averaged solution conformation of a unique bis-sulfated glycolipid (HSO3)2 -2,6Man,-2Glc,-1- sn -2,3- O -alkylglycerol, was studied in terms of the torsional angles of two glycosidic linkages, , (H1-C1-O-Cx) and , (C1-O-Cx-Hx), derived from heteronuclear three-bond coupling constants (3JC,H), and inter-residual proton,proton distances from J-HMBC 2D and ROESY experiments, respectively. The dihedral angles of Glc,1Gro in glycolipids were determined for the first time. The C1-C4 diagonal line of the ,-glucose ring makes an angle of ,,120 ° with the glycerol backbone, suggesting that the ,-glucose ring is almost parallel to the membrane surface in contrast with the perpendicular orientation of the ,-isomer. Furthermore, minimum-energy states around the conformation were estimated by Monte Carlo/stochastic dynamics (MCSD) mixed-mode simulations and the energy minimization with assisted model building and energy refinement (AMBER) force field. The Glc,1Gro linkage has a single minimum-energy structure. On the other hand, three conformers were observed for the Man,2Glc linkage. The flexibility of Man,2Glc was further confirmed by the absence of inter-residual hydrogen bonds which were judged from the temperature coefficients of the chemical shifts, d,/dT (,10,3 p.p.m.·°C,1), of hydroxy protons. The conformational flexibility may facilitate interaction of extracellular substances with both sulfate groups. [source] Investigation of excited-state properties of fluorene,thiophene oligomers by the SAC-CI theoretical approachJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 10 2010Potjaman Poolmee Abstract Excited states of fluorene-ethylenedioxythiophene (FEDOT) and fluorene- S,S -dioxide-thiophene (FTSO2) monomers and dimers were studied by the symmetry-adapted cluster (SAC)-configuration interaction (CI) method. The absorption and emission peaks observed in the experimental spectra were theoretically assigned. The first three excited states of the optimized conformers, and the conformers of several torsional angles, were computed by SAC-CI/D95(d). Accurate absorption spectra were simulated by taking the thermal average for the conformers of torsional angles from 0° to 90°. The conformers of torsional angles 0°, 15°, and 30° mainly contributed to the absorption spectra. The full width at half-maximum of the FEDOT absorption band is 0.60 eV (4839 cm,1), which agrees very well with the experimental value of 0.61 eV (4900 cm,1). The maximum absorption wavelength is located at 303 nm, which is close to those of the experimental band (327 nm). The calculated absorption spectrum of FTSO2 showed two bands in the range of 225,450 nm. This agrees very well with the available experimental spectrum of a polymer of FTSO2, where two bands are detected. The excited-state geometries were investigated by CIS/6-31G(d). These showed a quinoid-type structure which exhibited a shortening of the inter-ring distance (0.06 Å for FEDOT and 0.04 Å for FTSO2). The calculated emission energy of FEDOT is 3.43 eV, which agrees very well with the available experimental data (3.46 eV). The fwhmE is about 0.49 eV (3952 cm,1), while the experimental fwhm is 0.43 eV (3500 cm,1). For FTSO2, two bands were also found in the emission spectrum. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2010 [source] Estimation of the absolute internal-rotation entropy of molecules with two torsional degrees of freedom from stochastic simulationsJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 7 2005Eva Darian Abstract A method of statistical estimation is applied to the problem of evaluating the absolute entropy of internal rotation in a molecule with two torsional degrees of freedom. The configurational part of the entropy is obtained as that of the joint probability density of an arbitrary form represented by a two-dimensional Fourier series, the coefficients of which are statistically estimated using a sample of the torsional angles of the molecule obtained by a stochastic simulation. The internal rotors in the molecule are assumed to be attached to a common frame, and their reduced moments of inertia are initially calculated as functions of the two torsional angles, but averaged over all the remaining internal degrees of freedom using the stochastic-simulation sample of the atomic configurations of the molecule. The torsional-angle dependence of the reduced moments of inertia can be also averaged out, and the absolute internal-rotation entropy of the molecule is obtained in a good approximation as the sum of the configurational entropy and a kinetic contribution fully determined by the averaged reduced moments of inertia. The method is illustrated using Monte Carlo simulations of isomers of stilbene and halogenated derivatives of propane. The two torsional angles in cis -stilbene are found to be much more strongly correlated than those in trans -stilbene, while the degree of the angular correlation in propane increases strongly on substitution of hydrogen atoms with chlorine. © 2005 Wiley Periodicals, Inc. J Comput Chem 26: 651,660, 2005 [source] Structures and energies of D -galactose and galabiose conformers as calculated by ab initio and semiempirical methodsJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 7 2003Majda Rahal-Sekkal Abstract Optimized geometries and total energies of some conformers of ,- and ,- D -galactose have been calculated using the RHF/6-31G* ab initio method. Vibrational frequencies were computed at the 6-31G* level for the conformers that favor internal hydrogen bonding, in order to evaluate their enthalpies, entropies, Gibbs free energies, and then their structural stabilities. The semiempirical AM1, PM3, MNDO methods have also been performed on the conformers GG, GT, and TG of ,- and ,- D -galactose. In order to test the reliability of each semiempirical method, the obtained structures and energies from the AM1, PM3, and MNDO methods have been compared to those achieved using the RHF/6-31G* ab initio method. The MNDO method has not been investigated further, because of the large deviation in the structural parameters compared with those obtained by the ab initio method for the galactose. The semiempirical method that has yielded the best results is AM1, and it has been chosen to perform structural and energy calculations on the galabiose molecule (the disaccharides constituted by two galactose units , 1,4 linked). The goal of such calculations is to draw the energy surface maps for this disaccharide. To realize each map, 144 different possible conformations resulting from the rotations of the two torsional angles , and , of the glycosidic linkage are considered. In each calculation, at each increment of , and ,, using a step of 30° from 0 to 330°, the energy optimization is employed. In this article, we report also calculations concerning the galabiose molecule using different ab initio levels such as RHF/6-31G*, RHF/6-31G**, and B3Lyp/6-31G*. © 2003 Wiley Periodicals, Inc. J Comput Chem 24: 806,818, 2003 [source] Conformational analysis of thiopeptides: derivation of sp2 sulfur parameters for the CFF91 force fieldJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 10 2001Tran Trung Tran Abstract When a sulfur atom is used to substitute for the oxygen in peptide bonds, its bulkiness should restrict the conformational space available to an amino acid. This conformational restriction as well as the ability to confer resistance to enzymatic degradation in the body means that thio-substituted amino acids are potentially useful building blocks for drug design. To simulate the effects of thio substitution, force field parameters for sp2 sulfur are required. In this article, parameters for the thioamide group have been derived for the molecular mechanics CFF91 force field (available at http://www.ludwig.edu.au/archive/tran). The bond increment charges were obtained by fitting to ab initio charges and dipoles. The van der Waals parameters were obtained by fitting to high-resolution crystallographic data, and the nonbonded parameters were verified by comparing with experimentally derived lattice energy. The bonded parameters were derived by least-square fits to the ab initio calculated energy surfaces, i.e., conformational energy as well as their first and second derivatives of seven model thioamide molecules. When the sp2 sulfur parameters were tested on a set of seven X-ray crystallographic structures from the Cambridge Structural Database, they satisfactorily reproduced the bond lengths, bond angles, torsional angles, and nonbonded distances of all the crystal structures. © 2001 John Wiley & Sons, Inc. J Comput Chem 22: 1010,1025, 2001 [source] Synthesis, Structure and Emission Properties of Spirocyclic Benzofuranones and Dihydroindolones: A Domino Insertion,Coupling,Isomerization, Diels,Alder Approach to Rigid FluorophoresCHEMISTRY - A EUROPEAN JOURNAL, Issue 2 2008Daniel Abstract An alkynoyl ortho -iodo phenolester or alkynoyl ortho -iodo anilides and propargyl allyl ethers react under Sonogashira coupling conditions in the sense of an insertion,coupling,isomerization,Diels,Alder hetero domino reaction to furnish (tetrahydroisobenzofuran)-spirobenzofuranones and -spirodihydroindolones in good yields. Many representatives can be crystallized and single crystal structure analyses display steric and electronic substituent effects on the torsional angles of the terminal (hetero)aryl groups and the central cis,trans -butadiene fragment. DFT computations reveal that in the final pericyclic step the Diels,Alder termination is by far thermodynamically and kinetically favored over a possible Claisen rearrangement. Compounds of this new class of spirocyclic compounds possess large Stokes shifts and fluoresce intensively with blue over green to orange colors. As a consequence of the spirocyclic rigidity fluorescence lifetimes and quantum yields are rather high in some cases. Alkinoyl ortho -iodphenolester oder Alkinoyl ortho -iodanilide und Propargylallylether reagieren unter den Bedingungen der Sonogashira-Kupplung im Sinne einer Insertions,Kupplungs,Diels,Alder-Hetero-Domino-Reaktion zu (Tetrahydroisobenzofuran)-spirobenzofuranonen bzw. -spirodihydroindolonen in guten Ausbeuten, von denen viele kristallisiert werden konnten. Die Einkristallstrukturanalysen offenbaren sterische und elektronische Substituenteneffekte auf die Torsionswinkel der terminalen (Hetero)arylgruppen und des zentralen cis,trans -Butadienfragments. DFT-Rechnungen zeigen, dass im letzten pericyclischen Schritt die Diels,Alder-Reaktion gegenüber einer möglichen Claisen-Umlagerung bei weitem thermodynamisch und kinetisch begünstigt ist. Viele Verbindungen dieser neuen Spirocyclenklasse besitzen große Stokes-Verschiebungen und fluoreszieren intensive mit blauer, grüner oder oranger Farbe. Als Folge der spirocyclischen Rigidität sind in einigen Fällen die Fluoreszenzlebensdauern und Quantenausbeuten relative hoch. [source] Comparison of Properties of Aib-Rich Peptides in Crystal and Solution: A Molecular Dynamics StudyCHEMPHYSCHEM, Issue 5 2004Haibo Yu Abstract In order to study the differences of the structural properties of Aib-rich peptides in solution and in the crystalline state, molecular dynamics (MD) simulations of the Aib-containing peptide II (pBrBz-(Aib)5 -Leu-(Aib)2 -OMe) were performed in the crystalline state, starting from two different conformers obtained experimentally by X-ray diffraction. The structural properties as derived from X-ray crystallography (e.g., torsional angles and hydrogen bonds) are well-reproduced in both constant-volume and constant-pressure simulations, although the force-field parameters used result in a too-high density of the crystals. Through comparison with the results from previous MD and nuclear magnetic resonance (NMR) studies of the very similar peptide I (Z-(Aib)5 -Leu-(Aib)2 -OMe) in dimethylsulfoxide (DMSO) solution, it is found that, in the crystal simulation, the conformational distribution of peptide II is much narrower than that in the solution simulation of peptide I. This leads to a significant difference in 3J(HN, HC,) coupling constant values, in agreement with experimental data, whereas the NOE intensities or proton,proton distance bounds appear insensitive to the difference in conformational distribution. For small peptides the differences between their conformational distribution in the crystalline form and in solution may be much larger than for proteins, a fact which should be kept in mind when interpretating molecular properties in the solution state by using X-ray crystallographic data. [source] | ||||||||||