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Ramon Carbó-Dorca

Publications and source records attributed to Ramon Carbó-Dorca.

17 recordsLinked to original sources
PubMed2007

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). Both independent approaches are found to correlate very well, and both point toward decreasing aromaticity in any linear polyacenes upon going from the outer to inner rings.

Journal Article↗
PubMed2006

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,...,S(R). S0, of dimension d0, contains all configurations K with attributes (energy contributions, etc.) above thresholds tao 0 identical with{Tao 0(egy),Tao 0(etc.)}; the CI coefficients in S0 remain always free to vary. S1 accommodates Ks with attributes above tao 1 < or = tao 0. An eigenproblem of dimension d0 + d1 for S0 + S1 is solved first, after which the last d1 rows and columns are contracted into a single row and column, thus freezing the last d1 CI coefficients hereinafter. The process is repeated with successive Sj(j > or = 2) chosen so that corresponding CI matrices fit random access memory (RAM). Davidson's eigensolver is used R times. The final energy eigenvalue (lowest or excited one) is always above the corresponding exact eigenvalue in S. Threshold values {tao j;j = 0,1,2,...,R} regulate accuracy; for large-dimensional S, high accuracy requires S0 + S1 to be solved outside RAM. From there on, however, usually a few Davidson iterations in RAM are needed for each step, so that Hamiltonian matrix-element evaluation becomes rate determining. One mu hartree accuracy is achieved for an eigenproblem of order 24 x 10(6), involving 1.2 x 10(12) nonzero matrix elements, and 8.4 x 10(9) Slater determinants.

Journal Article↗
PubMed2006

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.

Journal Article↗
PubMed2004

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. The present procedure, implemented in Fortran 90 and named TGSA-Flex, is deeply detailed and tested over four molecular sets: amino acids, nordihydroguaiaretic acid (NDGA) derivatives, HIV-1 protease inhibitors, and 1-[2-hydroxyethoxy)methyl]-6-(phenylthio)thymine (HEPT) derivatives. TGSA-Flex performance is evaluated by means of computational time, number of superposed atoms (also comparing it with respect to the rigid approach), and index of fit between the compared structures.

Amino Acids↗
PubMed2004

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. The replacement of the oxo group by the thioxo group in position 4 on the benzoxazine ring of the antitubercular 3-(phenyl)-2H-benzoxazine-2,4(3H)-diones increases the activity, as well as the similar replacement in position 2.

Anti-Bacterial Agents↗
PubMed2003

Chemical structures from the analysis of domain-averaged Fermi holes: multiple metal-metal bonding in transition metal compounds.

The recently proposed approach based on the analysis of domain-averaged Fermi holes was applied to the study of the nature of metal-metal bonding in transition metal complexes and clusters. The main emphasis was put on the scrutiny of the systems assumed to contain direct multiple metal-metal bonds. The studied systems involve: (1) systems of the type M(2)X(6) (M = Mo, W, X = CH(3)) anticipated to contain metal-metal triple bonds; (2) the molecule of W(2)Cl(8) ((4-)) as the representative of the systems with quadruple metal-metal bonding; (3) diatomic molecules Mo(2) and V(2) considered as the potential candidates for higher than quadruple metal-metal bonding. Although the resulting picture of bonding has been usually shown to agree with the original expectations based on early simple MO models, some examples were also found in which the conclusions of the reported analysis display dramatic sensitivity to the quality of the wave function used for the generation of the Fermi holes. In addition to this we also report some examples where the original theoretical predictions of multiplicity of metal-metal bonds have to be corrected.

Journal Article↗
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 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. The accuracy and the predicting power of this new approach was tested on the comparison with a recent exhaustive study by Sullivan et al. It has been shown that the accuracy and the predicting power of both procedures is comparable, but, in contrast to a five-parameter correlation equation necessary to describe the data in the study, our approach is more simple and, in fact, only a simple one-parameter correlation equation is required.

Journal Article↗
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↗