We present three Slater-type atomic orbital (STO) valence basis (VB) sets for the first and second row atoms, referred to as the VB1, VB2, and VB3 bases. The smallest VB1 basis has the following structure: [3, 1] for the H and He atoms, [5, 1] for Li and Be, and [5, 3, 1] for the B to Ne series. For the VB2 and VB3 bases, both the number of shells and the number of functions per shell are successively increased by one with respect to VB1. With the exception of the H and Li atoms, the exponents for the VB1 bases were obtained by minimizing the sum of the Hartree-Fock (HF) and frozen-core singles and doubles configuration interaction (CISD FC) energies of the respective atoms in their ground state. For H and Li, we minimized the sum of the HF and CISD FC energies of the corresponding diatoms (i.e., of H(2) or Li(2)) plus the ground-state energy of the atom. In the case of the VB2 basis sets, the sum that was minimized also included the energies of the positive and negative ions, and for the VB3 bases, the energies of a few lowest lying excited states of the atom. To account for the core correlations, the VBx (x = 1, 2, and 3) basis sets for the Li to Ne series were enlarged by one function per shell. The exponents of these extended (core-valence, CV) basis sets, referred to, respectively, as the CVBx (x = 1, 2, and 3) bases, were optimized by relying on the same criteria as in the case of the VBx (x = 1, 2, and 3) bases, except that the full CISD rather than CISD FC energies were employed. We show that these polarized STO basis sets provide good HF and CI energies for the ground and excited states of the atoms considered, as well as for the corresponding ions.
DAMQT-2.1.0 is a new version of DAMQT package which includes topographical analysis of molecular electron density (MED) and molecular electrostatic potential (MESP), such as mapping of critical points (CPs), creating molecular graphs, and atomic basins. Mapping of CPs is assisted with algorithmic determination of Euler characteristic in order to provide a necessary condition for locating all possible CPs. Apart from the mapping of CPs and determination of molecular graphs, the construction of MESP-based atomic basin is a new and exclusive feature introduced in DAMQT-2.1.0. The GUI in DAMQT provides a user-friendly interface to run the code and visualize the final outputs. MPI libraries have been implemented for all the tasks to develop the parallel version of the software. Almost linear scaling of computational time is achieved with the increasing number of processors while performing various aspects of topography. A brief discussion of molecular graph and atomic basin is provided in the current article highlighting their chemical importance. Appropriate example sets have been presented for demonstrating the functions and efficiency of the code.
The performances of the algorithms employed in a previously reported program for the calculation of integrals with Slater-type orbitals are examined. The integrals are classified in types and the efficiency (in terms of the ratio accuracy/cost) of the algorithm selected for each type is analyzed. These algorithms yield all the one- and two-center integrals (both one- and two-electron) with an accuracy of at least 12 decimal places and an average computational time of very few microseconds per integral. The algorithms for three- and four-center electron repulsion integrals, based on the discrete Gauss transform, have a computational cost that depends on the local symmetry of the molecule and the accuracy of the integrals, standard efficiency being in the range of eight decimal places in hundreds of microseconds.
We present analytic refinements and applications of the deformed atomic densities method [Fernández Rico, J.; López, R.; Ramírez, G. J Chem Phys 1999, 110, 4213-4220]. In this method the molecular electron density is partitioned into atomic contributions, using a minimal deformation criterion for every two-center distributions, and the atomic contributions are expanded in spherical harmonics times radial factors. Recurrence relations are introduced for the partition of the two-center distributions, and the final radial factors are expressed in terms of exponential functions multiplied by polynomials. Algorithms for the practical implementation are developed and tested, showing excellent performances. The usefulness of the present approach is illustrated by examining its ability to describe the deformation of atoms in different molecular environments and the relationship between these atomic densities and some chemical properties of molecules.
The study of density and the role played by its atomic representation is proposed as a way for the rationalization of chemical behavior. As this behavior has been long rationalized in terms of the basic concepts of empirical structural chemistry, a direct link between both approaches is searched for by using the exact representation of the density provided by the deformed atoms in molecules method (Rico, J. F.; López, R.; Ema, I.; Ramírez, G.; Ludeña, E. J. Comput. Chem. 2004, 25, 1355-1363). Noting that the spherical terms of the pseudoatoms cannot be mainly responsible for the chemical behavior, we study the small nonspherical deformations and find that they reflect and support all basic concepts of empirical structural chemistry. Lone pairs; single, double, and triple bonds; different classes of atoms; functional groups; and so forth are paralleled by the density deformations in a neat manner. These facts are illustrated with several examples.
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