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Atomic Basins (atomic + basin)
Selected AbstractsAn efficient grid-based scheme to compute QTAIM atomic properties without explicit calculation of zero-flux surfacesJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 7 2009Juan I. Rodríguez Abstract We introduce a method to compute atomic properties according to the "quantum theory of atoms in molecules." An integration grid in real space is partitioned into subsets, ,i. The subset, ,i, is composed of all grid points contained in the atomic basin, ,i, so that integration over ,i is reduced to simple quadrature over the points in ,i. The partition is constructed from deMon2k's atomic center grids by following the steepest ascent path of the density starting from each point in the grid. We also introduce a technique that exploits the cellular nature of the grid to make the algorithm faster. The performance of the method is tested by computing properties of atoms and nonnuclear attractors (energies, charges, dipole, and quadrupole moments) for a set of representative molecules. © 2008 Wiley Periodicals, Inc. J Comput Chem 2009 [source] Charge density and electrostatic potential analyses in paracetamolACTA CRYSTALLOGRAPHICA SECTION B, Issue 3 2009Nouzha Bouhmaida The electron density of monoclinic paracetamol was derived from high-resolution X-ray diffraction at 100,K. The Hansen,Coppens multipole model was used to refine the experimental electron density. The topologies of the electron density and the electrostatic potential were carefully analyzed. Numerical and analytical procedures were used to derive the charges integrated over the atomic basins. The highest charge magnitude (,1.2,e) was found for the N atom of the paracetamol molecule, which is in agreement with the observed nucleophilic attack occurring in the biological media. The electric field generated by the paracetamol molecule was used to calculate the atomic charges using the divergence theorem. This was simultaneously applied to estimate the total electrostatic force exerted on each atom of the molecule by using the Maxwell stress tensor. The interaction electrostatic energy of dimers of paracetamol in the crystal lattice was also estimated. [source] Features of the electron density in magnesium diboride: reconstruction from X-ray diffraction data and comparison with TB-LMTO and FPLO calculationsACTA CRYSTALLOGRAPHICA SECTION B, Issue 5 2003S. Lee Features of the electron density in MgB2 reconstructed from room-temperature single-crystal X-ray diffraction intensities using a multipole model are considered. Topological analysis of the total electron density has been applied to characterize the atomic interactions in magnesium diboride. The shared-type B,B interaction in the B-atom layer reveals that both , and , components of the bonding are strong. A closed-shell-type weak B,B , interaction along the c axis of the unit cell has also been found. The Mg,B closed-shell interaction exhibits a bond path that is significantly curved towards the vertical Mg-atom chain ([110] direction). The latter two facts reflect two sorts of bonding interactions along the [001] direction. Integration of the electron density over the zero-flux atomic basins reveals a charge transfer of ,1.4,(1) electrons from the Mg atoms to the B-atom network. The calculated electric-field gradients at nuclear positions are in good agreement with experimental NMR values. The anharmonic displacement of the B atoms is also discussed. Calculations of the electron density by tight-binding linear muffin-tin orbital (TB-LMTO) and full-potential non-orthogonal local orbital (FPLO) methods confirm the results of the reconstruction from X-ray diffraction; for example, a charge transfer of 1.5 and 1.6 electrons, respectively, was found. [source] Resonance Structures of the Amide Bond: The Advantages of PlanarityCHEMISTRY - A EUROPEAN JOURNAL, Issue 27 2006Jon I. Mujika Abstract Delocalization indexes based on magnitudes derived from electron-pair densities are demonstrated to be useful indicators of electron resonance in amides. These indexes, based on the integration of the two-electron density matrix over the atomic basins defined through the zero-flux condition, have been calculated for a series of amides at the B3LYP/6-31+G* level of theory. These quantities, which can be viewed as a measure of the sharing of electrons between atoms, behave in concordance with the traditional resonance model, even though they are integrated in Bader atomic basins. Thus, the use of these quantities overcomes contradictory results from analyses of atomic charges, yet keeps the theoretical appeal of using nonarbitrary atomic partitions and unambiguously defined functions such as densities and pair densities. Moreover, for a large data set consisting of 24 amides plus their corresponding rotational transition states, a linear relation was found between the rotational barrier for the amide and the delocalization index between the nitrogen and oxygen atoms, indicating that this parameter can be used as an ideal physical-chemical indicator of the electron resonance in amides. [source] | ||||||||||