The Challenge of ab Initio Calculations in Small Neon Clusters.

Weakly bound neon dimer, trimer and tetramers are studied at HF and CCSD(T) levels using Dunning, ANO and SIGMA-s basis sets. Their ground-state binding energies are studied along with some structural properties. SIGMA-s basis sets have been developed explicitly for this issue but in a manner that can be readily applied to other atoms for the study of larger weakly bound systems. The difficulties for attaining accurate results on these systems are assessed by the computation of total, atomization and correlation energies, as well as equilibrium distances, with several basis sets of increasing size, ranging from non-augmented to double-augmented versions. Extrapolations are proposed to predict stabilization energies and the results are compared with previously published data.

Toward a Computational NMR Procedure for Modeling Dipeptide Side-Chain Conformation.

Theoretical relationships between the vicinal spin-spin coupling constants (SSCCs) and the χ1 torsion angles have been studied to predict the conformations of protein side chains. An efficient computational procedure is developed to obtain the conformation of dipeptides through theoretical and experimental SSCCs, Karplus equations, and quantum chemistry methods, and it is applied to three aliphatic hydrophobic residues (Val, Leu, and Ile). Three models are proposed: unimodal-static, trimodal-static-stepped, and trimodal-static-trigonal, where the most important factors are incorporated (coupled nuclei, nature and orientation of the substituents, and local geometric properties). Our results are validated by comparison with NMR and X-ray empirical data described in the literature, obtaining successful results on the 29 residues considered. Using out trimodal residue treatment, it is possible to detect and resolve residues with a simple conformation and those with two or three staggered conformers. In four residues, a deeper analysis explains that they do not have a unique conformation and that the population of each conformation plays an important role.

DAMQT 2.1.0: A new version of the DAMQT package enabled with the topographical analysis of electron density and electrostatic potential in molecules.

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.

Improved partition-expansion of two-center distributions involving Slater functions.

The calculation of the electronic structure of large systems is facilitated by the substitution of the two-center distributions by their projections on auxiliary basis sets of one-center functions. An alternative is the partition-expansion method in which one first decides what part of the distribution is assigned to each center, and next expands each part in spherical harmonics times radial factors. The method is exact, requires neither auxiliary basis sets nor projections, and can be applied to Gaussian and Slater basis sets. Two improvements in the partition-expansion method for Slater functions are reported: general expressions valid for arbitrary quantum numbers are derived and the efficiency of the procedure is increased giving analytical solutions to integrals previously computed by numerical quadrature. The efficiency of the new version is assessed in several molecules and the advantages over the projection methods are pointed out.

Chemical Notions from the Electron Density.

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.