Yeh and Berkowitz's scheme for 2D Ewald summaries is another general method for systems with slab geometry53. All simulations were performed in an NVT ensemble at a constant temperature of 298 K by using v-rescale thermostat54. The water contact angle θwas measured by fitting the time...
Since the parame- ter λ0 is small if the entropy loss during the bond for- mation is large, there must be a strong orientational or configurational constraint in the local geometry for the appearance of an hour-glass. Figure 4 shows the comparison 33 of theoretical cal- culation with the...
Diffraction Measurements. Single-crystal neutron diffraction data were collected at the hot-neutrons four-circle diffractometer D9 at Institut Laue Langevin (ILL, Grenoble, France) with a wavelength of 0.8322(1) Å obtained with a copper (220) monochromator operating in transmission geometry....
After the geometry and relaxation optimization of the system, an initial amorphous cell respectively containing 20 and 40 cellobioses was established, the energy was minimized and the density of model was adjusted to 1.59 g/cm3 [28]. After the above treatment, the established molecular model was...
The docking-predicted conformation of each compound was used as an input conformer for density functional theory (DFT) calculations using Gaussian 09 program package [38]. Complete geometry optimization was carried out with the DFT theory using B3LYP method based on the basis set 6-31g(d,p) ...
2.3. GED Structural Analysis Geometry of each conformer of the TPPN molecule possessed C1 symmetry and was described by 79 independent parameters. To reduce the correlation, the number of independent parameters was restricted to 14: Ct-CO4, CO4-CO3, O-CO1, CN3-C, C-N, Ct2-H bond ...
geometry optimization confirmed that the DP was an energy-minimum geometry directly connected to TS1 and that the energy of the DP calculated at the B3LYP/6-31+G(d,p) level of theory before energy corrections related to the ZPE and Gibbs energy was 3.44 kJ mol−1 lower than that of ...
This is easily understood from the molecular geometry: both the H+ and C2+ ions balance the momentum of I5+, but the H+ momenta are not included in the sum. This "dark" momentum is manifested as the shift of the correlated spot. However, it is also seen that the spot is well ...
The models were analyzed using the protein geometry function by MOE. There were no unacceptable deviations in the model and no outliers in the Ramachandran plot. Stability difference of amino acid substitution was calculated using Residue Scan function of MOE. 4.2. Preparation of Recombinant Proteins...
To confirm the optimized geometry of the title molecule, all stationary points are identified as minima. A triple split valence basis set along with a diffuse and polarization functions 6-311++G(d,p) basis set was used in all the calculations on the investigated systems. In order to arrive ...