Amphetamine-type stimulants (ATS) drug classification using shallow one-dimensional convolutional neural network.

Amphetamine-type stimulants (ATS) drug analysis and identification are challenging and critical nowadays with the emergence production of new synthetic ATS drugs with sophisticated design compounds. In the present study, we proposed a one-dimensional convolutional neural network (1DCNN) model to perform ATS drug classification as an alternative method. We investigate as well as explore the classification behavior of 1DCNN with the utilization of the existing novel 3D molecular descriptors as ATS drugs representation to become the model input.

Divagations about the periodic table: Boolean hypercube and quantum similarity connections.

In this study, several simple aspects associated with the periodic table (PT) of the elements are commented. First, the connection of the PT with the structure of a seven-dimensional Boolean hypercube leads afterward to discuss the nature of those PT elements bearing prime atomic numbers. Second, the use of quantum similarity (QS) to obtain an alternative insight on the PT element relations will be also developed.

Nine questions on energy decomposition analysis.

The paper collects the answers of the authors to the following questions: Is the lack of precision in the definition of many chemical concepts one of the reasons for the coexistence of many partition schemes? Does the adoption of a given partition scheme imply a set of more precise definitions of the underlying chemical concepts? How can one use the results of a partition scheme to improve the clarity of definitions of concepts? Are partition schemes subject to scientific Darwinism? If so, what is the influence of a community's sociological pressure in the "natural selection" process? To what extent does/can/should investigated systems influence the choice of a particular partition scheme? Do we need more focused chemical validation of Energy Decomposition Analysis (EDA) methodology and descriptors/terms in general? Is there any interest in developing common benchmarks and test sets for cross-validation of methods? Is it possible to contemplate a unified partition scheme (let us call it the "standard model" of partitioning), that is proper for all applications in chemistry, in the foreseeable future or even in principle? In the end, science is about experiments and the real world. Can one, therefore, use any experiment or experimental data be used to favor one partition scheme over another? © 2019 Wiley Periodicals, Inc.

Statistical-like signature of molecular basis sets.

This paper defines the construction of a sequence of functions that might be used to geometrically characterize any GTO set employed in any molecular calculation. Such functions characterizing a basis set act as molecular statistical-like elements: the arithmetic mean or centroid of the basis set, and also variance, skewness, and kurtosis, corresponding to the first terms of a possibly larger sequence of descriptor moments. Once the moment functions are built, then they can be integrated over their electron variables.

Aromaticity, quantum multimolecular polyhedra, and quantum QSPR fundamental equation.

A causal relation connecting aromaticity with the current aromaticity descriptors used in the literature and compliant with a quantum mechanics theoretical background is described.

Notes on quantitative structure-property relationships (QSPR), part 3: density functions origin shift as a source of quantum QSPR algorithms in molecular spaces.

A general algorithm implementing a useful variant of quantum quantitative structure-property relationships (QQSPR) theory is described. Based on quantum similarity framework and previous theoretical developments on the subject, the present QQSPR procedure relies on the possibility to perform geometrical origin shifts over molecular density function sets. In this way, molecular collections attached to known properties can be easily used over other quantum mechanically well-described molecular structures for the estimation of their unknown property values.

Softened electrostatic molecular potentials.

Electrostatic molecular potentials (EMPs) are studied from two points of view. First, a softened EMP (SEMP) approach is proposed, consisting in the substitution of a positive point charge as the entity with which an electronic density function (DF) interacts electrostatically to generate a classical EMP for a Gaussian charge distribution. Second, the performance of this SEMP approach under the Atomic Shell Approximation (ASA) is described and compared with classical EMP at the same ASA level.

Stereographic Projection of Density Functions (DF) and the Holographic Electronic Density Theorem (HEDT).

Mezey's holographic electronic density theorem is discussed from the point of view of stereographic projection techniques. Such a mathematical procedure is analyzed in depth from the point of view of first-order density functions; the procedure is then extended to any relevant quantum chemical function. This endeavor provides the background to construct a Holographic General Function Theorem (HGFT) for multivariate well-behaved functions.

The Fukui matrix: a simple approach to the analysis of the Fukui function and its positive character.

The Fukui matrix is introduced as the derivative of the one-electron reduced density matrix with respect to a change in the number of electrons under constant external potential. The Fukui matrix extends the Fukui function concept: the diagonal of the Fukui matrix is the Fukui function. Diagonalizing the Fukui matrix gives a set of eigenvectors, the Fukui orbitals, and accompanying eigenvalues.

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.

Commentaries on quantum similarity (1): Density gradient quantum similarity.

Computation of density gradient quantum similarity integrals is analyzed, while comparing such integrals with overlap density quantum similarity measures. Gradient quantum similarity corresponds to another kind of numerical similarity assessment between a pair of molecular frames, which contrarily to the usual up to date quantum similarity definitions are not measures, that is: strictly positive definite integrals. As the density gradient quantum similarity integrals are defined as scalar products of three real functions, they appear to possess a richer structure than the corresponding positive definite density overlap quantum similarity measures, while preserving the overall similarity trends, when the molecular frames are relatively moved in three-dimensional space.

Notes on quantitative structure-properties relationships (QSPR) part 2: the role of the number of atoms as a molecular descriptor.

A previous analysis performed in our laboratory about the polynomial dependency of the atomic quantum self-similarity measures on the atomic number, together with recent publications on quantitative structure-properties relationships (QSPR), based on the number of molecular atoms, published by various authors, have driven us to show here that a simplified form of the fundamental quantum QSPR (QQSPR) equation, permits to theoretically demonstrate the important, but obvious, role of the number of atoms in a molecule, as a possible molecular descriptor. A discussion of the practical use of the number of atoms in QSPR is also given at the end, which also contains a discussion on the role of Ockham's razor in descriptor simplification choices.

Notes on quantitative structure-properties relationships (QSPR) (1): A discussion on a QSPR dimensionality paradox (QSPR DP) and its quantum resolution.

Classical quantitative structure-properties relationship (QSPR) statistical techniques unavoidably present an inherent paradoxical computational context. They rely on the definition of a Gram matrix in descriptor spaces, which is used afterwards to reduce the original dimension via several possible kinds of algebraic manipulations. From there, effective models for the computation of unknown properties of known molecular structures are obtained.

Modeling the structure-property relationships of nanoneedles: A journey toward nanomedicine.

Innovative biomedical techniques operational at the nanoscale level are being developed in therapeutics, including advanced drug delivery systems and targeted nanotherapy. Ultrathin needles provide a low invasive and highly selective means for molecular delivery and cell manipulation. This article studies the geometry and the stability of a family of packed carbon nanoneedles (CNNs) formed by units of 4, 6, and 8 carbons, by using quantum chemistry computational modeling methods.

Critical thoughts on computing atom condensed Fukui functions.

Different procedures to obtain atom condensed Fukui functions are described. It is shown how the resulting values may differ depending on the exact approach to atom condensed Fukui functions. The condensed Fukui function can be computed using either the fragment of molecular response approach or the response of molecular fragment approach.

Critical analysis and extension of the Hirshfeld atoms in molecules.

The computational approach to the Hirshfeld [Theor. Chim. Acta 44, 129 (1977)] atom in a molecule is critically investigated, and several difficulties are highlighted.

Unrevealed structural requirements for auxin-like molecules by theoretical and experimental evidences.

An computational-biostatistical approach, supported by ab initio optimizations of auxin-like molecules, was used to find biologically meaningful relationships between quantum chemical variables and fresh bioassay's data. It is proven that the auxin-like recognition requires different molecular assembling states. We suggest that the carboxyl group is not the determining factor in explaining the biological auxin-like conduct.

Aromaticity in linear polyacenes: generalized population analysis and molecular quantum similarity approach.

The relative aromaticity of benzenoid rings in the linear polyacenes is investigated using two novel aromaticity approaches. According to the first, the aromaticity of individual benzene rings was gauged by the values of six-center bond indices (SCI) calculated within the so-called Generalized Population Analysis (GPA). In the second approach, the same goal is addressed using the theory of Molecular Quantum Similarity (MQS).

Select-divide-and-conquer method for large-scale configuration interaction.

A select-divide-and-conquer variational method to approximate configuration interaction (CI) is presented. Given an orthonormal set made up of occupied orbitals (Hartree-Fock or similar) and suitable correlation orbitals (natural or localized orbitals), a large N-electron target space S is split into subspaces S0,S1,S2,..

Coulomb and overlap self-similarities: a comparative selectivity analysis of structure-function relationships for auxin-like molecules.

Auxins are defined mainly by a set of physiological actions, but the structure-effect relationship still is based on chemical intuition. Currently a well-defined auxin molecular structure is not available. The existence of different auxin binding proteins and mechanisms of auxin action, the wide diversity of the auxin molecules, and the pleiotropic effects of auxin imply a completely different mechanism as described for the animal hormone concept.

Electron delocalization and aromaticity in linear polyacenes: atoms in molecules multicenter delocalization index.

Molecular aromaticity in the linear polyacenes is investigated using an atoms in molecules based six center index (SCI-AIM) which measures the electron delocalization. SCI-AIM values for the linear polyacenes indicate decreasing aromaticity going from outer to inner rings in the polyacene series. The SCI-AIM approach is compared to a Mulliken-like approach, and a critical comparison to the PDI index is made.

Similarity approach to QSAR. Application to antimycobacterial benzoxazines.

The antimycobacterial activity in six series of substituted 3-phenyl-2H-benzoxazine-2,4(3H)-dithiones and 3-(phenyl)-4-thioxo-2H-benzoxazine-2,4(3H)-diones has been studied using a quantum molecular similarity approach. The approach is based on the use of fragment self-similarity measures as new universal molecular descriptors applicable for the design of novel theoretical QSAR models. Using this approach it was possible to show that while traditional QSAR models were able to describe the activity only within each of the six sets of studied molecules individually, the proposed approach is much more general and a single universal QSAR model describing the activity of all the 39 studied molecules in all the studied series together was built.

TGSA-Flex: Extending the capabilities of the Topo-Geometrical Superposition Algorithm to handle flexible molecules.

In this work, an extension of the already studied Topo-Geometrical Superposition Approach (TGSA) is presented. TGSA, a general-purpose, fast, automatic, and user-intuitive three-dimensional molecular alignment procedure, was originally designed to superpose rigid molecules simply based on atomic numbers, molecular coordinates, and connectivity. The algorithm is further developed to enable handling rotations around single bonds; in this way, common structural features, which were not properly aligned due to conformational causes, can be brought together, thus improving the molecular similarity picture of the final alignment.

Molecular basis of LFER. Modeling of the electronic substituent effect using fragment quantum self-similarity measures.

A new approach allowing the theoretical modeling of the electronic substituent effect is proposed. The approach is based on the use of fragment Quantum Self-Similarity Measures (MQS-SM) calculated from domain averaged Fermi Holes as new theoretical descriptors allowing for the replacement of Hammett sigma constants in QSAR models. To demonstrate the applicability of this new approach its formalism was applied to the description of the substituent effect on the dissociation of a broad series of meta and para substituted benzoic acids.