Quality of approximate electron densities and internal consistency of molecular alignment algorithms in molecular quantum similarity

Description of non-covalent interactions in benzyl chalcocyanate crystals from smoothed Cromer-Mann electron density distribution functions

A well-known method to characterize non-covalent interactions consists in the topological analysis of electron density distribution (EDD) functions, complemented by the search for minima in the reduced density gradient (RDG) distributions. Here, we characterize intermolecular interactions occurring in crystals of benzyl chalcocyanate compounds through bond critical points (BCP) of the promolecular electron density (ED) built from the crystallographic Cromer-Mann parameters, at several smoothing levelst. The trajectories formed by thet-dependent BCP locations are interpreted in terms of the intermolecular interactions occurring within the crystal arrangements. Chalcogen…nitro BCPs are clearly present in the unsmoothed EDDs but are annihilated astincreases, while chalcogen…chalcogen BCPs appear and are among the only BCPs left at the highest smoothing level. The chalcogen bonds are differentiated from the other chalcogen interactions through the linear chalcogen…BCP…nitro geometry at low smoothing level and their more negative Laplacian values. The annihilation of CPs can be followed by the apparition of a RDG minimum, associated with a very weak interaction. Along the BCP trajectories, the Laplacian shows a progressive concentration of the ED in the intermolecular space within the crystals and adopts the most negative values at the shortest atom…atom separations. At the termination point of a BCP trajectory, the drastic increase of the ellipticity value illustrates the flattening of the EDD.

HÜCKEL TREATMENT OF PYRROLE AND PENTALENE AS A FUNCTION OF CYCLOPENTADIENYL USING LOCAL QUANTUM SIMILARITY INDEX (LQSI) AND THE TOPO-GEOMETRICAL SUPERPOSITION APPROACH (TGSA)

In this paper some of the characteristic of Hückel method, were exploited in order to obtain some important results, through a new technique with which it is possible to obtain non-degenerate characteristic values as in the case of pyrrole and allowing the expression of conjugated ring systems (Pentalene) as function of a system of diene monomer (Cyclopentadienyl). The local similarity index based on the Hirshfeld partitioning in the framework of conceptual Density Functional Theory (DFT), was introduced in the secular determinant of the Hückel method and was applied to Pyrrole molecule in order to express their orbital energies as a function of the orbital energy of Cyclopentadienyl, to express the energies of molecular orbitals of the Cyclopentadienyl as a function of Pentalene, resolved by the Hückel method and applied to Cyclopentadienyl, by means of six local similarity index: Overlap, Overlap-Interaction, Coulomb, Coulomb-Interaction, with their respective Euclidean distances, using the Topo-Geometrical Superposition Approach (TGSA) as a method of alignment, which allowed us to obtain good results in local similarity indices.

This technique will permit the study of some molecular systems that differ in one atom in its molecular structure, resolving the Hückel method for the Pyrrole and Thiophene system without taking into account the considerations with its neighboring atoms. This proposed technique reduces the symmetry of fused ring systems which are Cyclopentadienyl derivatives, allowing to express the orbital energy of a diene dimmer (Pentalene) as a function of diene monomer systems, creating a tool of calculation to solve the problem of obtaining non-degenerate values in systems where the approximations in the Hückel method approximation provide degenerate values and providing a symmetry reduction technique.

Communications on quantum similarity, part 3: a geometric-quantum similarity molecular superposition algorithm

This work describes a new procedure to obtain optimal molecular superposition based on quantum similarity (QS): the geometric-quantum similarity molecular superposition (GQSMS) algorithm. It has been inspired by the QS Aufbau principle, already described in a previous work, to build up coherently quantum similarity matrices (QSMs). The cornerstone of the present superposition technique relies upon the fact that quantum similarity integrals (QSIs), defined using a GTO basis set, depend on the squared intermolecular atomic distances. The resulting QSM structure, constructed under the GQSMS algorithm, becomes not only optimal in terms of its QSI elements but can also be arranged to produce a positive definite matrix global structure. Kruskal minimum spanning trees are also discussed as a device to order molecular sets described in turn by means of QSM. Besides the main subject of this work, focused on MS and QS, other practical considerations are also included in this study: essentially the use of elementary Jacobi rotations as QSM refinement tools and inward functions as QSM scaling methods.

Pattern recognition based on color-coded quantum mechanical surfaces for molecular alignment

A pattern recognition algorithm for the alignment of drug-like molecules has been implemented. The method is based on the calculation of quantum mechanical derived local properties defined on a molecular surface. This approach has been shown to be very useful in attempting to derive generalized, non-atom based representations of molecular structure. The visualization of these surfaces is described together with details of the methodology developed for their use in molecular overlay and similarity calculations. In addition, this paper also introduces an additional local property, the local curvature (C (L)), which can be used together with the quantum mechanical properties to describe the local shape. The method is exemplified using some problems representing common tasks encountered in molecular similarity.

Molecular Quantum Similarity and Chirality: Enantiomers with Two Asymmetric Centra

Molecular quantum similarity is evaluated for enantiomers possessing two asymmetric carbon atoms, namely halogen substituted ethanes. This study is an extension of previous work performed on molecules with a single asymmetric carbon atom and molecules possessing a chiral axis. Global similarity and its local counterpart based on the Hirshfeld partitioning are evaluated. By these means we quantify the dissimilarity of enantiomers and illustrate Mezey's holographic electron density theorem in chiral systems. Furthermore, the relation between the optical activity and the dissimilarity is studied. Special attention is drawn to the meso compounds, since these isomers enable us to examine local chirality in an achiral system.

Molecular Quantum Similarity of Enantiomers: Substituted Allenes

Molecular quantum similarity is evaluated for enantiomers in the case of molecules possessing a chiral axis, as an extension of previous studies on molecules with a single asymmetric carbon atom. As a case study, the enantiomers of substituted allenes are examined. Next to studying global similarity, using the already existing similarity indices defined by Carbó and Hodgkin-Richards, we evaluate local similarity using our earlier proposed local similarity index based on the Hirshfeld partitioning, to quantify the consequences of Mezey's holographic electron density theorem in chiral systems. Furthermore, the relation between the optical activity and the dissimilarity is studied.

Influence of conformation on the representation of small flexible molecules at low resolution: alignment of endothiapepsin ligands

In this contribution, we discuss a molecular representation mode for the generation of reduced descriptions of flexible molecules in various conformations. The representations of the endothiapepsin ligands are constituted by graphs of peaks obtained through a hierarchical merging algorithm which combines the location of promolecular electron density (ED) maxima with the decomposition of the molecular structures into fragments. The representations are then aligned through the use of a Monte Carlo/Simulated Annealing procedure. The evaluation function of the alignment solutions is based on the local density values of the peaks and their inter-distances. The applications show that the alignment of a given molecule onto itself, in a different conformation, is successful when a pseudo-topological path length is considered in the evaluation function of the solution, while Cartesian distances are more adapted to the scoring for alignments of two different molecules in their co-crystallized conformation. Results are compared with the available literature data.