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Ramon Carbó-Dorca

Publications and source records attributed to Ramon Carbó-Dorca.

10 recordsLinked to original sources
PubMed2002

Molecular quantum similarity and the fundamentals of QSAR.

A general overview on quantum similarity and applications to QSAR is presented. The concepts regarding quantum similarity from its theoretical foundation and consecutive development, involving mathematical formulation and similarity measures, are presented and complemented with application examples. The practical part, based on the well-known Crammer 31 steroids set, covers approximate quantum similarity calculations, molecular superposition, and statistics. In this way, the reader will find both basic general information and applicability of quantum similarity.

Animals↗
PubMedDate not supplied

Molecular basis of linear free energy relationships. The nature of inductive effect in aliphatic series.

The nature of inductive substituent effect on the acidity of aliphatic carboxylic acids was analyzed in terms of a quantum chemical model based on the Longuet-Higgins theory of proton affinity. It has been shown that the effect is generally composed of two additive components, the electrostatic one and the polarization one. The relative weights of these components depend in any given case on the type of the reaction series. Thus, for example, the substituent-induced variation of gas-phase acidity in a series of 4-substituted bicyclo[2.2.2]octane-1-carboxylic acids is due to the electrostatic component classically described by the Kirkwood-Westheimer theory. On the other hand, the gas-phase basicity in a series of aliphatic amines is primarily determined by the polarization term that in traditional description corresponds to the concept of inductive effect.

Journal Article↗
PubMedDate not supplied

Using molecular quantum similarity measures under stochastic transformation to describe physical properties of molecular systems.

The application of molecular quantum similarity measures (MQSM) to correlate physicochemical properties is reported. Satisfactory quantitative structure-property relationship (QSPR) models are obtained for three molecular sets, where boiling points and chromatographic retention times and indices are studied. In this work, MQSM are scaled using a stochastic transformation and related to molecular properties using the partial least-squares technique.

Journal Article↗
PubMedDate not supplied

Modeling large macromolecular structures using promolecular densities.

A procedure to easily construct fitted density functions is presented. This methodology, based on the promolecule approach, is able to handle large macromolecular systems, such as proteins. The usual procedure dealing with fitted densities has been improved by adding some restrictions, which allow faster calculations. As a main application example, molecular isodensity contours (MIDCOs) are constructed for two proteins, one of them composed of more than 50 000 atoms. MIDCOs, as a visual representation of the molecular density function, and thus an important descriptor of the molecular charge distribution, constitute a powerful tool in the understanding of molecular systems. MIDCOs are presented for both proteins, allowing exploration of their surfaces, as well as analysis of their shapes. Also, as a quantum mechanical calculation example, molecular quantum self-similarity measures are calculated for several proteins.

Computer Simulation↗
PubMedDate not supplied

Molecular quantum similarity-based QSARs for binding affinities of several steroid sets.

The application of Molecular Quantum Similarity Measures (MQSM) to correlate biological activities for three different sets of steroids is reported. A general protocol for the generation of descriptors is detailed, thus covering molecular superposition, electronic density fitting, and quantum similarity calculation issues. Satisfactory Quantitative Structure-Activity Relationship (QSAR) models (r(2) in [0.69,0.94] and q(2) in [0.59,0.73]), comparable to previous studies, are obtained in all cases, where steroid binding affinities to different enzymes are studied. In this work, MQSM, properly scaled using Carbó Index, are related to activity using a Partial Least Squares routine.

Aromatase↗
PubMedDate not supplied

Fast calculation of quantum chemical molecular descriptors from the electronegativity equalization method.

The use of the Electronegativity Equalization Method (EEM) is presented for high performance calculation of molecular electrostatic descriptors, giving quite similar results to those obtained through Density Functional Theory (B3LYP/6-31G*) calculations. Molecular descriptors include atomic charges and different related descriptors as well as Fukui functions, hardness and softness.

Journal Article↗
PubMedDate not supplied

Molecular quantum similarity analysis of estrogenic activity.

The main objective of this study was to evaluate the capability of 120 aromatic chemicals to bind to the human alpha estrogen receptor (hER alpha) by the use of quantum similarity methods. The experimental data were segregated into two categories, i.e., those compounds with and without estrogenicity activity (active and inactive). To identify potential ligands, semiquantitative structure-activity relationships were developed for the complete set correlating the presence or lack of binding affinity to the estrogen receptor with structural features of the molecules. The structure-activity relationships were based upon molecular similarity indices, which implicitly contain information related to changes in the electron distributions of the molecules, along with indicator variables, accounting for several structural features. In addition, the whole set was split into several chemical classes for modeling purposes. Models were validated by dividing the complete set into several training and test sets to allow for external predictions to be made.

Estrogens, Non-Steroidal↗
PubMedDate not supplied

Quantum similarity superposition algorithm (QSSA): a consistent scheme for molecular alignment and molecular similarity based on quantum chemistry.

The use of the molecular quantum similarity overlap measure for molecular alignment is investigated. A new algorithm is presented, the quantum similarity superposition algorithm (QSSA), expressing the relative positions of two molecules in terms of mutual translation in three Cartesian directions and three Euler angles. The quantum similarity overlap is then used to optimize the mutual positions of the molecules. A comparison is made with TGSA, a topogeometrical approach, and the influence of differences on molecular clustering is discussed.

Aldosterone↗
PubMedDate not supplied

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

The calculation of molecular quantum similarity measures using the molecular electron density requires the electron density and molecular alignment between two molecules. To obtain meaningful quantum similarity matrices, the electron density should be calculated efficiently and accurately and the alignment should be internally consistent. The internal consistency of the alignment for a series of molecules is investigated through distance geometry concepts. The calculation of the quantum similarity matrix requires the calculation of a quadratic number of similarity integrals, and a scheme to obtain these efficiently is developed. Both the alignment procedure and the ASA method for approximate molecular electron densities are tested for a set of steroid molecules.

Journal Article↗