Force field parameters for rotation around chi torsion axis in nucleic acids

To raise the accuracy of the force field for nucleic acids, several parameters were elaborated, focusing on the rotation around chi torsion axis. The reliability of molecular dynamics (MD) simulation was significantly increased by improving the torsion parameters at C8--N9--C1'--X (X = H1', C2', O4') in A, G and those at C6--N1--C1'--X in C, T, and U. In this work, we constructed small models representing the chemical structure of A, G, C, T, and U, and estimated energy profile for chi-axis rotation by executing numerous quantum mechanical (QM) calculations. The parameters were derived by discrete Fourier transformation of the calculated QM data. A comparison in energy profile between molecular mechanical (MM) calculation and QM one shows that our presently derived parameters well reproduce the energy surface of QM calculation for all the above torsion terms. Furthermore, our parameters show a good performance in MD simulations of some nucleic acids. Hence, the present refinement of parameters will enable us to perform more accurate simulations for various types of nucleic acids.     

Unique Thermal Structural Phase Transitions Exhibited by Unsymmetrical Organometallic Gold(III)-Dithiolene Complexes with Pentylthio and Hexylthio Groups

Unsymmetrical gold(III)-dithiolene complexes are potential candidates for molecular materials that exhibit thermal structural phase transitions. In this study, unsymmetrical ppy-gold(III) (ppy⁻=C-deprotonated-2-phenylpyridine(−)) complexes [AuC5] and [AuC6] coordinated by dithiolene ligands containing tetrathiafulvalene (TTF) skeletons with pentylthio (2-{bis(pentylthio)-1,3-dithiol-2-ylidene}-1,3-dithiol-4,5-dithiolate(2−)) and hexylthio groups (2-{bis(hexylthio)-1,3-dithiol-2-ylidene}-1,3-dithiol-4,5-dithiolate(2−)) were synthesized. Both complexes exhibited a large absorption band at approximately 508 nm, owing to intramolecular ligand-to-ligand charge transfer. One-dimensional columnar structures with head-to-tail molecular arrangements around the metal ions were constructed in the crystals. The flexible alkylthio groups were intercalated into crystalline spaces between dithiolene ligands in the columns. [AuC5] exhibits a simple phase transition at 198 °C between crystalline and isotropic phases irreversibly. The crystalline phase of [AuC6] observed at 25 °C melted at 148 °C. Another crystalline phase grew above 148 °C with a very slow crystallization rate from the liquid phase and was completely transformed into an isotropic phase at 200 °C.     

Space-time analytic smoothing effect for the pseudo-conformally invariant Schrödinger equations

We study the global Cauchy problem for the mass critical nonlinear Schrödinger equations. We prove the global existence of analytic solutions in both space and time variables for sufficiently small and exponentially decaying Cauchy data. The method of proof depends on the Leibniz rule for the generator of pseudo-conformal transforms at the L ² critical level.     

Implementation of pi-pi interactions in molecular dynamics simulation

No explicit pi-pi interaction term has been incorporated in the conventional molecular dynamics (MD) simulation programs in spite of its significant role in the folding of biomolecules and the clustering of organic chemicals. In this article, we propose a technique to emphasize the effect of pi-pi interactions using a function of energy and implement it into an MD simulation program. Several trial calculations show that the pi-pi incorporated program gives improved results consistent with experimental data on atom geometry and has no unfavorable interference with the conventional computational framework. This indicates an importance of the explicit consideration of pi-pi interactions in MD simulation.     

Density functional theory investigation of novel Eu(III) complexes with asymmetric bis(phosphine) oxides

Recently, we have developed novel Eu(III) complexes with three beta-diketonates and one asymmetric bis(phosphine) oxide whose light emission intensity is drastically increased. In this paper, one of these complexes is investigated by the density functional theory calculation. Sixteen isomers of this complex have been considered. The ratio of the existence for the most stable isomer (B1_1a) is found to be about 51%, and the sum of the ratio of the existence for the six most stable isomers (B1_1a, B1_3a, B1_8a, B1_2a, B1_1b, and B1_5a) is about 100%, assuming the Boltzmann distribution (T = 300 K). The coordination structures of the six most stable isomers in the ground states are similar, and we can expect asymmetric ligand fields for them, favorable for the efficient light emission. Vertical excitation energies and oscillator strengths for each isomer have been obtained by the time-dependent density functional theory. With the red-shift of the wavelength and the interpolation by Gaussian convolution, both the calculated absorption spectra for the most stable isomer B1_1a and the calculated absorption spectra for the ensemble average of the isomers are found to be similar to the experimental fluorescence excitation spectra. The efficiency of energy transfer from the triplet excited state to the Eu(III) ion is considered by calculating DeltaEET (difference between the adiabatic excitation energy of the complex for the lowest triplet state and the emission energy of the Eu(III) ion for 5D0 to 7F2). The characters for the lowest triplet states for the isomers are investigated by the spin density distributions of the triplet states.     

Biosynthesis of violacein: a genuine intermediate, protoviolaceinic acid, produced by VioABDE, and insight into VioC function

A biosynthetic intermediate of violacein produced by the mixed enzymes of VioABDE was elucidated to be 5-(5-hydroxy-1H-indol-3-yl)-3-(1H-indol-3-yl)-1H-pyrrole-2-carboxylic acid, named protoviolaceinic acid, indicating that VioC, responsible for the final biosynthetic step, works to oxygenate at the 2-position of the right side indole ring, and that the oxygenation reaction to form the central pyrrolidone core proceeds in a non-enzymatic fashion.     

Synthesis of the entire carbon framework of the kedarcidin chromophore aglycon

In advanced studies directed toward the total synthesis of the kedarcidin chromophore, we have successfully achieved the late-stage installation of the nine-membered diyne ring in the presence of the highly functionalised ansamacrocyclic bridge.     

Methoxy- and fluorine-substituted analogs of O-1302: synthesis and in vitro binding affinity for the CB1 cannabinoid receptor

Methoxy and fluorine analogs substituted on the terminal carbon of the pentyl chain of N-(piperidinyl)-1-(2,4-dichlorophenyl)-4-methyl-5-(4-pentylphenyl)-1H-pyrazole-3-carboxamide (O-1302) were synthesized in a multi-step process from 5-phenyl-1-pentanol, which was based on the 1,5-diarylpyrazole core template of N-(piperidinyl)-5-(4-chlorophenyl)-1-(2,4-dichlorophenyl)-4-methyl-1H-pyrazole-3-carboxamide (SR141716) through condensation of the respective amine with pyrazole carboxylic acid, in order to develop tracers for medical imaging. Their potency for inhibiting the binding of the CB1 antagonist [(3)H]SR141716 was evaluated with the aim of developing positron emission tomography (PET) ligands for the cerebral cannabinoid CB1 receptor. These analogs bearing a piperidinyl carboxamide at the C(3) of the pyrazole ring exhibited affinities comparable to those of the CB1 reference antagonist SR141716, which warrants further investigation using the radiolabeled form for biological imaging studies. A morpholine ring substituted at the C(3) of the pyrazole ring resulted in a reduction of the CB1 affinity.     

Boron 1s photoelectron spectrum of 11BF3: vibrational structure and linewidth

The boron 1s photoelectron spectrum of (11)BF(3) has been measured at a photon energy of 400 eV and a resolution of about 55 meV. The pronounced vibrational structure seen in the spectrum has been analyzed to give the harmonic and anharmonic vibrational frequencies of the symmetric stretching mode, 128.1 and 0.15 meV, as well as the change in equilibrium BF bond length upon ionization, -5.83 pm. A similar change in bond length has been observed for PF(3) and SiF(4), but a much smaller change for CF(4). Theoretical calculations for BF(3) that include the effects of electron correlation give results that are in reasonable accord with the experimental values. The Lorentzian (lifetime) width of the boron 1s core hole in BF(3) is found to be 72 meV, comparable to the value of 77 meV that has been reported for CF(4).