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Minimum-energy Structure (minimum-energy + structure)
Selected AbstractsGlobal Minimum-Energy Structure and Spectroscopic Properties of I2.,,n,H2O Clusters: A Monte Carlo Simulated Annealing StudyCHEMPHYSCHEM, Issue 1 2010Arup Kumar Pathak Abstract The vibrational (IR and Raman) and photoelectron spectral properties of hydrated iodine-dimer radical-anion clusters, I2.,,n,H2O (n=1,10), are presented. Several initial guess structures are considered for each size of cluster to locate the global minimum-energy structure by applying a Monte Carlo simulated annealing procedure including spin,orbit interaction. In the Raman spectrum, hydration reduces the intensity of the II stretching band but enhances the intensity of the OH stretching band of water. Raman spectra of more highly hydrated clusters appear to be simpler than the corresponding IR spectra. Vibrational bands due to simultaneous stretching vibrations of OH bonds in a cyclic water network are observed for I2.,,n,H2O clusters with n,3. The vertical detachment energy (VDE) profile shows stepwise saturation that indicates closing of the geometrical shell in the hydrated clusters on addition of every four water molecules. The calculated VDE of finite-size small hydrated clusters is extrapolated to evaluate the bulk VDE value of I2., in aqueous solution as 7.6 eV at the CCSD(T) level of theory. Structure and spectroscopic properties of these hydrated clusters are compared with those of hydrated clusters of Cl2., and Br2.,. [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] IR/Raman spectroscopy and DFT calculations of cyclic di-amino acid peptides.JOURNAL OF RAMAN SPECTROSCOPY, Issue 11 2009Part III: comparison of solid state, solution structures of cyclo(L -Ser- L -Ser) Abstract B3-LYP/cc-pVDZ calculations of the gas-phase structure and vibrational spectra of the isolated molecule cyclo(L -Ser- L -Ser), a cyclic di-amino acid peptide (CDAP), were carried out by assuming C2 symmetry. It is predicted that the minimum-energy structure is a boat conformation for the diketopiperazine (DKP) ring with both L -seryl side chains being folded slightly above the ring. An additional structure of higher energy (15.16 kJ mol,1) has been calculated for a DKP ring with a planar geometry, although in this case two fundamental vibrations have been calculated with imaginary wavenumbers. The reported X-ray crystallographic structure of cyclo(L -Ser- L -Ser), shows that the DKP ring displays a near-planar conformation, with both the two L -seryl side chains being folded above the ring. It is hypothesized that the crystal packing forces constrain the DKP ring in a planar conformation and it is probable that the lower energy boat conformation may prevail in the aqueous environment. Raman scattering and Fourier-transform infrared (FT-IR) spectra of solid state and aqueous solution samples of cyclo(L -Ser- L -Ser) are reported and discussed. Vibrational band assignments have been made on the basis of comparisons with the calculated vibrational spectra and band wavenumber shifts upon deuteration of labile protons. The experimental Raman and IR results for solid-state samples show characteristic amide I vibrations which are split (Raman: 1661 and 1687 cm,1, IR: 1666 and 1680 cm,1), possibly due to interactions between molecules in a crystallographic unit cell. The cis amide I band is differentiated by its deuterium shift of ,30 cm,1, which is larger than that previously reported for trans amide I deuterium shifts. A cis amide II mode has been assigned to a Raman band located at 1520 cm,1. The occurrence of this cis amide II mode at a wavenumber above 1500 cm,1 concurs with results of previously examined CDAP molecules with low molecular weight substituents on the C, atoms, and is also indicative of a relatively unstrained DKP ring. Copyright © 2009 John Wiley & Sons, Ltd. [source] Global Minimum-Energy Structure and Spectroscopic Properties of I2.,,n,H2O Clusters: A Monte Carlo Simulated Annealing StudyCHEMPHYSCHEM, Issue 1 2010Arup Kumar Pathak Abstract The vibrational (IR and Raman) and photoelectron spectral properties of hydrated iodine-dimer radical-anion clusters, I2.,,n,H2O (n=1,10), are presented. Several initial guess structures are considered for each size of cluster to locate the global minimum-energy structure by applying a Monte Carlo simulated annealing procedure including spin,orbit interaction. In the Raman spectrum, hydration reduces the intensity of the II stretching band but enhances the intensity of the OH stretching band of water. Raman spectra of more highly hydrated clusters appear to be simpler than the corresponding IR spectra. Vibrational bands due to simultaneous stretching vibrations of OH bonds in a cyclic water network are observed for I2.,,n,H2O clusters with n,3. The vertical detachment energy (VDE) profile shows stepwise saturation that indicates closing of the geometrical shell in the hydrated clusters on addition of every four water molecules. The calculated VDE of finite-size small hydrated clusters is extrapolated to evaluate the bulk VDE value of I2., in aqueous solution as 7.6 eV at the CCSD(T) level of theory. Structure and spectroscopic properties of these hydrated clusters are compared with those of hydrated clusters of Cl2., and Br2.,. [source] N2O in small para -hydrogen clusters: Structures and energeticsJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 6 2009Hua Zhu Abstract We present the minimum-energy structures and energetics of clusters of the linear N2O molecule with small numbers of para -hydrogen molecules with pairwise additive potentials. Interaction energies of (p- H2),N2O and (p- H2),(p- H2) complexes were calculated by averaging the corresponding full-dimensional potentials over the H2 angular coordinates. The averaged (p- H2),N2O potential has three minima corresponding to the T-shaped and the linear (p- H2),ONN and (p- H2),NNO structures. Optimization of the minimum-energy structures was performed using a Genetic Algorithm. It was found that p- H2 molecules fill three solvation rings around the N2O axis, each of them containing up to five p- H2 molecules, followed by accumulation of two p- H2 molecules at the oxygen and nitrogen ends. The first solvation shell is completed at N = 17. The calculated chemical potential oscillates with cluster size up to the completed first solvation shell. These results are consistent with the available experimental measurements. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2009 [source] | ||||||||||