Biomedical subjects

Ricardo A Mosquera

Publications and source records attributed to Ricardo A Mosquera.

11 recordsLinked to original sources

PubMed2007

QTAIM N-center delocalization indices as descriptors of aromaticity in mono and poly heterocycles.

The implementation of the n-center electron delocalization indices, n-DIs, and n-order electron localization indices, n-LIs, within the framework of the quantum theory of atoms in molecules, QTAIM, is performed. n-DIs are shown to be very useful to study the local aromaticity in monocyclic and polycyclic compounds. Total and pi n-DIs from n=4 to 7 were computed for a series of typical 4, 5, 6, and 7-center aromatic and antiaromatic rings. For n>or=5 the pi n-DI accounts for the 95% of the total n-DI and can be employed alone to measure the aromaticity. A scaling factor on the n-DIs is required in order to compare the aromaticity of [5c-6e] and [6c-6e] rings, the same correction allows to estimate the relative aromatic stabilization of polycyclic compounds using the sum of its values for individual rings. This is called Effective Scaled Electron Delocalization, ESED. The comparison with other aromaticity indices reflects a good correlation between ESED and both resonance energies, and HOMA indices. The most important differences between scaled pi n-DIs and NICS(0) indices are found for compounds that contain rings with different number of centers or pi electrons.

Journal Article↗

PubMed2006

On the electronic origin of strain energy: QTAIM study of perfluorocycloalkanes.

The strain energies (SE) of the five smallest perfluorocycloalkanes (c-CnF2n; n=3, 4, 5, 6, and 7) were calculated by means of several homodesmotic processes using B3LYP/6-31++G(d,p) optimized molecular energies. These values were compared with the energy difference between the linear and cyclic CF2 groups calculated by means of the quantum theory of atoms in molecules (QTAIM) applied on charge densities obtained at the same computational level. The differences between the values computed with both methods vary from 255 (n=3) to 629 (n=7) kJ mol-1. These differences arise because QTAIM-computed SE contain the energy involved in opening the ring to give rise to nearly transferable central CF2 fragments of linear perfluoroalkanes, whereas homodesmotic energies contain energy terms corresponding to transformation of nontransferable linear CF2 fragments and a ring-opening energy, which depending on the process, transforms CF2 cyclic compounds into nearly transferable or nontransferable linear CF2 groups.

Journal Article↗

PubMed2006

Hartree-Fock energy partitioning in terms of Hirshfeld atoms.

A Hirshfeld decomposition scheme of the Hartree-Fock total molecular energy into atomic energies is presented. The calculations are performed by direct numerical integration and the results are compared for a set of 28 molecules containing different kinds of atoms. The calculated atomic energies show a strong dependency on changes of atomic electron population and hybridization. Linear correlations are found between the energy and the population for H, these being related to the electronegativity of this atom and to the external potential created by the remaining atoms. The proposed energy partitioning scheme appears to be useful for studies such as proton acidity, the anomeric effect and group transferability, and allows atomic virial ratios to be obtained. Finally, the atomic potential energies are found to mimic trends based on exact expressions as well as trends displayed by molecular quantities, thus lending credibility to the partitioning scheme used.

Journal Article↗

PubMed2006

On the electron donor and the electrophilic substitution activating abilities of substituents in uracil.

QTAIM properties for uracil and 18 derivatives containing the substituents -NH(2), -OH, -OCH(3), -SH, -F, -Cl, -CH(3) -NO(2), and -Li in position 5 or 6 were computed on MP2/6-31++G//MP2/6-31G charge densities. The results indicate that -OH, -OCH(3), and -NH(2) groups are really retrieving charge from the ring. Also, the activating ability of the substituent groups, usually considered as the variation of electron population at the carbon where the electrophilic attack takes place, C, was studied. The study shows that the activating ability is reflected by the variation of pi charge or quadrupole moment at C, and also by the variation of the Laplacian of the charge density in the secondary charge concentration points around C (SCC-C). They indicate a similar, but not exactly equal, graduation of activating ability. The relative behavior of the substituents is basically the same as in benzene, though benzene has more tendency to concentrate charge in the SCC-C regions than uracil, where this tendency is larger for 6- than for 5-derivatives. sigma(+/-)(R) Taft parameters are found to display good correlations with the above indicated activating indexes. Finally, the resonance model predicts most of the main variations displayed by QTAIM atomic pi electron populations of derivatives with regard to uracil, but there are still some significant variations of the pi electron charge that it cannot predict.

Computer Simulation↗

PubMed2005

Joint QTAIM and Hirshfeld study of the sigma and pi charge distribution and electron delocalization in carbonyl compounds: a comparative study with the resonance model.

Atomic charges and delocalization indexes (DIs) for a series of carbonyl compounds comprising dimethyl ketone, acetaldehyde, acetic acid, methyl acetate, acetamide, methyl vinyl ketone, divinyl ketone, and benzoic acid were studied using two different atomic partitionings: the QTAIM and the Hirshfeld (stockholder) scheme. The resonance model, traditionally employed to explain the reactivity of these compounds, is not in line with the total atomic charges and DIs calculated by both methodologies. However, the resonance model is supported to some extent by the pi charges and pi DIs calculated by both schemes, but the calculated values indicate that the pi population delocalizes only to a small degree. Although the absolute values of QTAIM and stockholder atomic charges are significantly different, the pi charges and the values of the DIs show similar trends for all the atoms and molecules of this study; this is especially the case for the pi DIs. A study of the electron density on the level of a single MO performed for CO, H2CO, F2CO, and H2CS reveals that the differences in the atomic sigma charges computed with both partitionings can be traced back to their different treatment of interatomic regions.

Journal Article↗

PubMed2005

Quantum theory of atoms in molecules analysis on the conformational preferences of vinyl alcohol and related ethers.

Vinyl alcohol, methyl vinyl ether, and tert-butyl vinyl ether were studied within the framework of the quantum theory of atoms in molecules at the B3LYP/6-311++G(2d,2p) level. Local and integrated properties of the charge density indicate that the anti conformational preference of the tert-butyl derivative is not due to a differing resonance contribution with regard to the less bulky vinyl ethers but to steric effects. There is a small delocalization of charge density, either total or pi, between oxygen and the terminal vinyl carbon, which does not support the resonance picture of vinyl compounds.

Journal Article↗

PubMed2005

Topological study of intramolecular hydrogen bonding in beta-hydroxyethylperoxy radical and beta-hydroxyethoxy radical along its dissociation pathway.

The presence of intramolecular hydrogen bond (IHB) in beta-hydroxyethylperoxy and beta-hydroxyethoxy radicals was investigated using the QTAIM topological study on UB3LYP/6-311++G(2d,2p) charge densities. Only one of the two conformers of beta-hydroxyethylperoxy radical which were previously considered to present IHB displays a bond critical point (BCP) associated to an IHB. Furthermore, the atomic energies and electron populations indicate no evidence of IHB in the second conformer. Nevertheless, very small differences in molecular energies were obtained using several one-step and multi-step methods (G3, G3B3) between both conformers. No BCP is found between the hydroxyl hydrogen and the oxygen in the most stable conformer or in the transition state for the dissociation path of beta-hydroxyethoxy radical. However, a BCP is formed in the last steps of this path, thereby yielding H-bonded products.

Ethylene Glycols↗

PubMed2005

On the applicability of resonance forms in pyrimidinic bases. II. QTAIM interpretation of the sequence of protonation affinities.

The atomic properties of neutral and protonated forms of uracil and some model compounds, computed from B3LYP/6-31++G//B3LYP/6-31G charge densities with the QTAIM theory, indicate that sigma electron reorganization plays a significant role in the protonation processes. This reorganization is substantially different for O=C-C=C and O=C-C-X (X = N, O) units, involving transfers of electron population between all atoms in the first case but not across the C-X bond in the second unit. O-Protonation is basically favored over the N-protonation because of the lower electron population transferred to the proton. The stability sequence of N-protonated forms can be rationalized in terms of the closer position of the proton, when attached to N3, to regions of larger electron population (carbonyl groups).

Amino Acids↗

PubMed2004

Theoretical study of the electronic structure of CnS (n=1-6) thiocumulenes.

Linear sulfur-carbon chains C(n)S (n=1-6) of astronomical interest were examined by means of several theoretical methods. The three smallest compounds of the series were chosen to evaluate the performance of several computational models, including Hartree-Fock theory, density functional theory with the Becke's three parameter exchange functional and the correlation functional of Lee, Yang, and Parr (B3LYP), and electron-correlated methods (second-order Moller-Plesset perturbation method (MP2), configuration interaction method including single and double excitations (CISD), and quadratic configuration interaction method including single and double excitations (QCISD) in combination with a large variety of basis sets. The systematic comparison between the experiment and theory indicates that the B3LYP/6-311G** method can be considered suitable for the study of the electronic structures of the C(n)S compounds. The electronic ground states of the C(n)S molecules alternate between 1Sigma and 3Sigma for odd and even values of n, respectively. The B3LYP/6-311G** wave functions for these electronic ground states were analyzed by means of the atoms in molecules (AIM) and natural bond orbital (NBO) methods. Both approaches suggest that the electronic structures for the singlet and triplet compounds must be considered separately. According to the NBO method, singlet compounds can be properly represented by acetylenic structures with alternating single and triple bonds (S[triple bond]C-C[triple bond]C...). However, triplet compounds are better described by means of double bond-double bond cumulenic structures (S=C=C=C=C...) as a consequence of the average between different alpha and beta electronic densities. AIM delocalization indexes and NBO interactions between localized orbitals also indicate that these structures are strongly pi delocalized. Finally, the different singlet and triplet structures proposed provide a consistent explanation for the geometries, dipole moments, and spin-density values of the C(n)S compounds studied.

Journal Article↗

PubMed2003

A box-counting-based algorithm for computing Shannon entropy in molecular dynamics simulations.

A box-counting-based algorithm (SEBC) has been developed for the numerical computation of the Shannon entropy from samples of continuous functions. Its performance was tested by applying it to several samples of known continuous distribution functions. The results obtained with SEBC reproduced those obtained by analytical or numerical integration. SEBC was also employed for computing the Shannon entropies of the steric energy, Sh(E(S)), of several amino acids from their in vacuo NVE molecular dynamics simulations using the AMBER-4 force field. The results obtained correlate linearly with the experimental standard thermodynamic entropies of these compounds. This work points to the possibility of introducing straightforward and reliable calculations of thermodynamic entropies from empirical linear relationships with Sh(E(S)) obtained from MD simulations.

Journal Article↗

PubMedDate not supplied

Do the neighboring residues in a polypeptide affect the electron distribution of an amino acid significantly? A quantitative study using the quantum theory of atoms in molecules (QTAIM).

Geometries, as well as bond and atomic properties obtained with the atoms-in-molecules theory applied on B3LYP/6-31++G//B3LYP/6-31G charge densities, of the N-formyl amides of the nine tripeptides obtained by combining glycine, alanine, and serine around a central glycine residue were analyzed to check how the properties of the central residue are modified by other amino acids bonded to it. All of the molecules were optimized from an alpha-helix conformation that was also displayed by the optimized structure. Significant variations of the geometry (especially remarkable for dihedral angles) and atomic properties of the central glycine residue are observed when it is attached to a serine residue whose side chain is involved in a hydrogen bond.

Amino Acids↗