1,721,030 research outputs found
Ab initio-based intermolecular carbon–carbon pair potentials for polycyclic aromatic hydrocarbon clusters
No full textWe derived the carbon-carbon pair potentials for polycyclic aromatic hydrocarbon (PAH) Clusters, which exhibited a strikingly similar geometry to that of the two-layer graphite. The binding energy of PAH clusters ranging in size from the benzene chiner to the pyrene chiner obtained by ab initio calculations at the MP2 level was used to extract the pair potentials in the form of the Lennard-Jones and Exponential-6 functions. Identical binding energy and equilibrium interlayer distance were reproduced by these functions to those calculated by the ab initio method. The pair potentials for PAHs yield the same equilibrium C-C distance as the known pair potentials for graphite and fullerenes, but nearly twice the well depth because of the polarization of the C-H bond. (C) 2005 American Institute of Physics.open111314sciescopu
Dynamics Measurement of Diffusing Single-Molecule with Tens of Millisecond Observation Time by Liposome Tethering
No full text11sciescopu
Ab initio studies on the van der Waals complexes of polycyclic aromatic hydrocarbons. I. Benzene-naphthalene complex
No full textThe stable geometries and binding energies of the benzene-naphthalene complex were studied by the point-by-point method using ab initio calculations at the MP2/6-31G*(0.25) and MP2/6-31+G* levels. Medium-size basis sets were employed not only to save computational time but also to compensate for the tendency of the MP2 method to overestimate the electron correlation energy of aromatic clusters. The use of the 6-31G*(0.25) and 6-31+G* basis sets in the test calculation for the benzene dimer yielded results very similar to those from the CCSD(T) calculation. As for the benzene-naphthalene complex, four stable geometries were found: one parallel-displaced type and three T-shaped ones, with each type similar to the case of the benzene dimer. The global minimum was found to be the parallel-displaced structure whose energy was -4.88 kcal/mol at the MP2/6-31G*(0.25) level and -3.94 kcal/mol at the MP2/6-31+G* level. These values are similar to1.9 times that of the benzene dimer on the same level of calculation. The energy of the most stable T-shaped structure was -4.17 and -3.47 kcal/mol at the MP2/6-31G*(0.25) and MP2/6-31+G* levels, respectively, which are similar to1.8 times that of the corresponding T-shaped structure of the benzene dimer. (C) 2002 American Institute of Physics.open114242sciescopu
Ab initio studies on the van der Waals complexes of polycyclic aromatic hydrocarbons. II. Naphthalene dimer and naphthalene-anthracene complex
No full textAb initio calculations were carried out for the naphthalene dimer and naphthalene-anthracene complex to determine their stable geometries and binding energies. Two medium-size basis sets of 6-31G*(0.25) and 6-31+G* were employed at the MP2 level. Five local minima were found for the naphthalene dimer, three of which were parallel-displaced type and the other two T-shaped type. The global minimum geometry was a parallel-displaced structure of a two-layer graphitic type (C-i point group), not the crossed form (D-2d). Its energy calculated by the 6-31G*(0.25) and 6-31+G* basis sets was -7.62 and -6.36 kcal/mol, respectively. The naphthalene-anthracene complex showed four local minima, two of which were parallel-displaced type and the other two T-shaped type. The global minimum was a twisted parallel-displaced form (C-2), in which the centers of both molecules lie on the same z-axis with their two long axes skewed at an angle of approximate to40degrees. Its energy was -11.30 and -9.52 kcal/mol with the 6-31G*(0.25) and 6-31+G* basis sets, respectively. From these results a set of general rules for the stable geometry of the polycyclic aromatic hydrocarbon clusters were derived, which turned out to be the same as those previously deduced from other systems less directly relevant to polycyclic aromatic hydrocarbons: (1) a face-to-face configuration is unstable, (2) the T-shaped structure is stable, (3) the parallel-displaced structure is also stable. We also found some additional rules: (4) the energies of the T-shaped and parallel-displaced structures are quite comparable when the molecules are small, but (5) the parallel-displaced structure becomes more stable than the T-shaped one as the molecules become larger due to the nature of the pi-pi interaction. The interplanar distance of stable parallel-displaced structures was about 3.3-3.4 Angstrom, while the plane-to-center distances of T-shaped structures was about 5.0-5.1 Angstrom. We also discovered what we would call the integer rule for the binding energy of the polycyclic aromatic hydrocarbon clusters in that the binding energy varied linearly as the number of overlapping hexagons in the parallel-displaced structures. The ratio of binding energies for the benzene dimer, benzene-naphthalene complex, naphthalene dimer, and naphthalene-anthracene complex were nearly 1:2:3:4. (C) 2002 American Institute of Physics.open116974sciescopu
Photoelectron spectroscopy of pyrazine anion clusters
No full textWe studied the energetics and character of electron binding in the pyrazine anion clusters by mass spectrometry, photoelectron spectroscopy, and theoretical calculations. The mass distribution showed that the minimum number of molecules in a neat cluster of pyrazine to form an anion was two, with a single pyrazine molecule incapable of accommodating an excess electron. On the other hand, even the addition of a very weak solvent such as Ar sufficed to bring the affinity level of pyrazine below the vacuum level. Photoelectron spectra of some pyrazine-containing anion clusters, (Pz)(1)(-)-Ar-n (n=1-10) and (Pz)(1)(-)-S-1 (S=pyrazine, benzene, and water), were obtained. A vibrational progression was observed in the photoelectron spectra of (Pz)(1)(-)-Ar-n. The electron affinity of pyrazine was determined to be -0.01+/-0.01 eV from extrapolation. A small drop in incremental electron affinity was observed from (Pz)(1)(-)-Ar-4 to (Pz)(1)(-)-Ar-5, indicating closure of the first solvation shell by four Ar atoms. The pyrazine dimer anion was found to exist in two isomeric forms of comparable energy, one with a symmetric structure and the other with an asymmetric one. The hydrogen bonding with the ring nitrogen strongly affects the binding of the pyrazine dimer anions. The electron affinity of the pyrazine dimer was estimated to be 0.13-0.15 eV. (C) 2002 American Institute of Physics.open111920sciescopu
Real-time submillisecond single-molecule FRET dynamics of freely diffusing molecules with liposome tethering
Full text linkSingle-molecule fluorescence resonance energy transfer (smFRET) is one of the powerful techniques for deciphering the dynamics of unsynchronized biomolecules. However, smFRET is limited in its temporal resolution for observing dynamics. Here, we report a novel method for observing real-time dynamics with submillisecond resolution by tethering molecules to freely diffusing 100-nm-sized liposomes. The observation time for a diffusing molecule is extended to 100 ms with a submillisecond resolution, which allows for direct analysis of the transition states from the FRET time trace using hidden Markov modelling. We measure transition rates of up to 1,500 s(-1) between two conformers of a Holliday junction. The rapid diffusional migration of Deinococcus radiodurans single-stranded DNA-binding protein (SSB) on single-stranded DNA is resolved by FRET, faster than that of Escherichia coli SSB by an order of magnitude. Our approach is a powerful method for studying the dynamics and movements of biomolecules at submillisecond resolution.open112420sciescopu
FOLDING OF 8-17 DEOXYRIBOZYME STUDIED BY THREE-COLOR ALTERNATING-LASER EXCITATION OF SINGLE MOLECULES
No full textThe folding of 8-17 deoxyribozyme was investigated by three-color alternating-laser excitation (3c-ALEX), a new single-molecule fluorescence resonance energy transfer (FRET) method we recently developed. Since 3c-ALEX has the capability of simultaneously sorting fluorescent molecules based on their labeling status and monitoring three interprobe distances of a biomolecule by employing three-color FRET, it is an ideal tool to study folding of multibranched molecules. The 8-17 deoxyribozyme, a DNA enzyme that cleaves a specific RNA substrate, is a good model system for a multibranched molecule, since it. has the structure of a three-way DNA junction with a bulge. Labeling all three branches of the 8-17 with different fluorescent probes, we studied its [Mg2+]-dependent folding in a Na+ buffer solution. With the stoichiometric sorting capability of 3c-ALEX, we first selected only the triply labeled 8-17 in a solution of all heterogeneous mixtures and then simultaneously measured all three interprobe distances of the selected species. Our results show that the 8-17 folds into a pyramidal form upon increasing [Mg2+]], in a similar way with [Zn2+] as found in an earlier study conducted at the ensemble level. The apparent dissociation constant of Mg2+ was more than 100 times larger than that of Zn2+ and showed considerable variance with buffer concentration. No clear sign of two-step folding was observed for Mg2+, in contrast to the case of Zn2+. Compared with the hammerhead ribozyme, the 8-17 was found to require 10 times higher [Mg2+] to undergo folding. By comparison with the folding of several inactive 8-17 analogues, we found that the two conserved sequences (A and G) of the triad loop of the shortest branch are critical elements for folding, especially for the folding at low [Mg2+]. Our results suggest that the role of the stem loop is to provide a scaffold for the two bases to be properly positioned for the necessary interaction and that the two bases are directly involved in the interaction that plays a critical role in folding. This work demonstrates that 3c-ALEX is a powerful single-molecule method to study the structure and folding of complex and multibranched biomolecules.X113417sciescopu
TREATMENT OF CONTACT TRACTION AT THE DIE - WORKPIECE INTERFACE FOR THE ELASTIC ANALYSIS OF DIE DEFORMATION
No full textA method to calculate the contact traction on the die-workpiece interface is proposed. A systematic method for performing the elastic finite element analysis of the die deformation by using the information obtained from the finite element analysis of the workpiece deformation is proposed. The proposed method can be applied to both the two-dimensional and three-dimensional analyses of die deformation independently of the friction modelling and the constitutive equations. A rigid-plastic finite element analysis of workpiece deformation is carried out for the upsetting of a cylindrical workpiece. In order to check the validity of the present method for both flat and curved contact surfaces, the elastic finite element analysis of die deformation is then performed for flat square block forging as well as for a bevel gear forging (Yoon and Yang, Int. J. Mech. Sci. 32, 277-291, 1990) [8]. From the computation it is shown that the error due to the transfer of data from the workpiece mesh to the die mesh does not influence appreciably the elastic deformation of the die. The proposed method can be applied to arbitrarily curved die geometries in three-dimensional metal forming problems
Three-dimensional simulation for non-isothermal forging of a steam turbine blade by the thermoviscoplastic finite element method
No full textThe study is concerned with the three-dimensional analysis for non-isothermal forging of a steam turbine blade by the thermoviscoplastic finite element method. The analysis includes deformation of the workpiece and heat transfer of the workpiece and the die. In the transient heat-transfer analysis, the finite element method is adopted for the workpiece, while the boundary element method is adopted for the die. The non-isothermal analysis is compared with the isothermal analysis as well as with the experimental results. The length of the forged blade increases by 20 per cent as compared to the initial billet, as confirmed by the deformed configuration of both the computation and experiment
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