Biomedical subjects

J Sánchez-Marín

Publications and source records attributed to J Sánchez-Marín.

5 recordsLinked to original sources

PubMed2006

Lower Rydberg series of methane: a combined coupled cluster linear response and molecular quantum defect orbital calculation.

Vertical excitation energies as well as related absolute photoabsorption oscillator strength data are very scarce in the literature for methane. In this study, we have characterized the three existing series of low-lying Rydberg states of CH4 by computing coupled cluster linear response (CCLR) vertical excitation energies together with oscillator strengths in the molecular-adapted quantum defect orbital formalism from a distorted Cs geometry selected on the basis of outer valence green function calculations. The present work provides a wide range of data of excitation energies and absolute oscillator strengths which correspond to the Rydberg series converging to the three lower ionization potential values of the distorted methane molecule, in energy regions for which experimentally measured data appear to be unavailable.

Journal Article↗

PubMed2005

Multistate active spaces from local CAS-SCF molecular orbitals: the photodissociation of HFCO as an example.

A recently developed algorithm to generate localized molecular orbitals (LMO) is applied to the study of excited states along a photodissociation process. The LMOs allow for the selection of a consistent complete active space (CAS) for the simultaneous description of all the electronic states involved in a multistate process on the basis of simple chemical criteria. The local nature of the orbitals is used to label them in a unique way that does not depend on the molecular geometry. The selection of the electronic configurations of interest for the set of target states on only the basis of the dominant excitations required by the simplest configuration interaction (CI) descriptions for both ground and excited states is fairly simplified. The following of the changes in the nature of the states along cuts in the set of potential energy surfaces (PES) is also simpler. The C--F bond breaking and the states involved in the photodissociation of the HFCO system, together with another geometrical path along the PES of the same previous states, are studied by way of examples in this work. The local nature of the MOs warrants that this small system is representative enough to show the advantages of the procedure and that its application to larger systems (R-FCO systems) would be straightforward.

Journal Article↗

PubMed1998

Characterizing cavities in model inclusion molecules: a comparative study.

We have selected fullerene-60 and -70 cavities as model systems in order to test several methods for characterizing inclusion molecules. The methods are based on different technical foundations such as a square and triangular tessellation of the molecule taken as a unitary sphere, spherical tessellation of the molecular surface, numerical integration of the atomic volumes and surfaces, triangular tessellation of the molecular surface, and a cubic lattice approach to a molecular space. Accurate measures of the molecular volume and surface area have been performed with the pseudo-random Monte Carlo (MCVS) and uniform Monte Carlo (UMCVS) methods. These calculations serve as a reference for the rest of the methods. The SURMO2 and MS methods have not recognized the cavities and may not be convenient for intercalation compounds. The programs that have detected the cavities never exceed 5% deviation relative to the reference values for molecular volume and surface area. The GEPOL algorithm, alone or combined with TOPO, shows results in good agreement with those of the UMCVS reference. The uniform random number generator provides the fastest convergence for UMCVS and a correct estimate of the standard deviations. The effect of the internal cavity on the accessible surfaces has been calculated.

Algorithms↗

PubMed1996

Torsional effects on the molecular polarizabilities of the benzothiazole (A)-benzobisthiazole (B) oligomer A-B13-A.

We outline a method for the calculation of multipole moments and molecular dipole-dipole (alpha), dipole-quadrupole (A), and quadrupole-quadrupole (C) polarizabilities, which we have successfully applied to benzothiazole (A)-benzobisthiazole (B) oligomer A-B13-A. Three model rotational isomers have been characterized: (1) the fully planar (000) rotational isomer; (2) a conformation with each unit rotated 10 degrees in the alternate direction (+(-)+), and (3) a rotational isomer with each unit rotated 10 degrees in the same direction (+3). The dipole moment, mu, is smaller for isomers 000 and +(-)+ than for isomer +3. The calculation of alpha A, and C has been performed by use of the interacting induced dipoles polarization model, which calculates tensor effective anisotropic point polarizabilities (method of Applequist). The values of alpha, A, and C are in the same order of magnitude as reference calculations (PAPID) program). The values of A are rather sensitive to mu, which varies under rotation, explaining the greatest value of magnitude of Ax,xx for polar isomer +3. This rotational isomer has the maximum hydrophilic accessible surface, which would improve solubility in water. It is found that small torsional changes can enhance solubility by increasing the hydrophilic accessible surface without too much affecting the values of alpha and C. However, the torsion of the oligomer can vary the value of mu and so modify A.

Benzothiazoles↗

PubMed1991

Improved AMYR program: an algorithm for the theoretical simulation of molecular associations, including geometrical and topological characterization of the dimers.

Program AMYR, originally written by S. Fraga (University of Alberta, Canada), allows for the calculation of molecular associations using a pair-wise atom-atom potential. The interaction energy is evaluated through a 1/R expansion. Our improved version includes a dispersion energy term in the potential corrected by damping functions, the possibility of carrying out energy minimizations through variable metric methods, as well as the optional calculation of geometrical and topological indices. Program AMYR has been adapted also for high-performance computing and vectorization. An interactive version of the program carries out real-time molecular graphics showing simultaneously the energy profile of the calculations.

Algorithms↗