Electrostatic filed

Taking the inverse Fourier transformation we obtain the electrostatic filed under water confinement in explicit form ... 

The diabatic free energy profile obtained by the method is plotted in Figures 2.11. The most notable feature of the figures is that it is essentially parabolic with respect to the reaction coordinate. This is nothing but the manifestation of the central limiting theorem, and the results indicate that the response of solvent fluctuation to the electrostatic filed is linear. The behavior, however, is not trivial, because the free energy calculated via Eqs. (2.61) and (2.62) are inherently non-linear. 

If the MM+ option to n sc bond dipoles for nonbonded electrostatic calculation s is set, then MM-t-ignores atomic charges but uses dipole m om en ts supplied in its parameter set (in themmpstr. files ). 

In stead, the electrostatic con tribn tion conies from definin g a set of bond dipole moments associated woth polar bonds. These bond moments are defined in the m m psir.LxL(dbf) file along with the bond stretching parameters and are given in units of Debyes. The cen ter of th e dipole Is defined to be th e m Idpoint of the bond an d two dipoles p. and pj. separated by Rjj. as shown beltnv ... 

Once the job is completed, the UniChem GUI can be used to visualize results. It can be used to visualize common three-dimensional properties, such as electron density, orbital densities, electrostatic potentials, and spin density. It supports both the visualization of three-dimensional surfaces and colorized or contoured two-dimensional planes. There is a lot of control over colors, rendering quality, and the like. The final image can be printed or saved in several file formats. 

In addition to total energy and gradient, HyperChem can use quantum mechanical methods to calculate several other properties. The properties include the dipole moment, total electron density, total spin density, electrostatic potential, heats of formation, orbital energy levels, vibrational normal modes and frequencies, infrared spectrum intensities, and ultraviolet-visible spectrum frequencies and intensities. The HyperChem log file includes energy, gradient, and dipole values, while HIN files store atomic charge values. 

For a quantum mechanical calculation, the single point calculation leads to a wave function for the molecular system and considerably more information than just the energy and gradient are available. In principle, any expectation value might be computed. You can get plots of the individual orbitals, the total (or spin) electron density and the electrostatic field around the molecule. You can see the orbital energies in the status line when you plot an orbital. Finally, the log file contains additional information including the dipole moment of the molecule. The level of detail may be controlled by the PrintLevel entry in the chem.ini file. 

Edit Output File icon xlix effective core potentials 101 electron affinity 142 electron correlation 6, 114,118 electron density 165 electron spin 259 electronic structure theory 3 electrostatic potential-derived charges CHelpG 196... 

K+ channels selectively transport K+ across membranes, hyperpolarize cells, set membrane potentials and control the duration of action potentials, among a myriad of other functions. They use diverse forms of gating, but they all have very similar ion permeabilities. All K+ channels show a selectivity sequence of K+ Rb+ > Cs+, whereas the transport of the smallest alkali metal ions Na+ and Li+ is very slow—typically the permeability for K+ is at least 104 that of Na+. The determination of the X-ray structure of the K+-ion channel has allowed us to understand how it selectively filters completely dehydrated K+ ions, but not the smaller Na+ ions. Not only does this molecular filter select the ions to be transported, but also the electrostatic repulsion between K+ ions, which pass through this molecular filter in Indian file, provides the force to drive the K+ ions rapidly through the channel at a rate of 107-108 per second. (Reviewed in Doyle et al., 1998 MacKinnon, 2004.)... 

Thorner, D.A., Willett, P., Weight, P.M., and Taylor, R. Similarity searching in files of three-dimensional chemical structures Representation and searching of molecular electrostatic potentials using field-graphs./. Comput.-Aided Mol. Des. 1997, 3 3, 163-174. 

Technically, the AM1/DFT correction is now implemented as a combination of the structure analysis tool COSMO/yze developed for COSMO/rag and the MOPAC2002 program [59]. COSMO/y-ze analyses the bond types of a new protein and writes an input file for MOPAC, which contains all the correction charges for atoms and bond centers. By a small modification, MOPAC2002 is now able to read these AM1/DFT correction charges and to add the corresponding corrections to the electrostatic potential on the COSMO surface at the end of a MOPAC/COSMO calculation. In a final COSMO call, the improved potential is converted into updated COSMO charges and a COSMO file with quality closer to BP-SVP quality is written. 

Finally, the use of a u-polarity field instead of different and more empirical electrostatic, hydrophobic, and hydrogen-bonding fields should lead to considerable advantages in molecular field analysis (MFA) techniques such as ComFA. On the one hand, a includes all three aspects of interactions in a single field, and on the other hand, this interaction picture meanwhile is much better validated quantitatively than the empirical fields presently used in MFA. The only problem here is that a is a surface property and thus less a field in space. With some effort it should be possible to develop reasonable functions for the extension of a perpendicular to the molecular surface and thus to generate a kind of 3D a-filed as required for MFA. 

Wild, D.J. and Willett, P. Similarity Searching in Files ofThree-Dimensional Chemical Structures Alignment of Molecular Electrostatic Potentials with a Genetic Algorithm. J. Chem. Inf. Comput. Sci., 1996,36, 159-167. 

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