Biomedical subjects

E Francisco

Publications and source records attributed to E Francisco.

18 recordsLinked to original sources

PubMed2007

Chemical fragments in real space: definitions, properties, and energetic decompositions.

The physical and chemical meaning of real space molecular fragments resulting from arbitrary partitions of the density is reviewed under a common unifying formalism. Both fuzzy (interpenetrating) and non-fuzzy (exhaustive) decompositions are treated on an equal basis. Density decompositions are consistently generalized to compatible density matrix partitions by using Li and Parr's ideas (Li and Parr J Chem Phys 1986, 84, 1704), and these are carried onto an energy partition. It is argued that the merits of a given decomposition should be judged against both the charge and the energetic image it provides. Atomic partitions are used to show how the interacting quantum atoms approach (IQA) allows us to cope with the most important energy cancellations of quantum chemistry. Binding results from a trade-off between atomic (or fragment) energy deformations with respect to a reference and interatomic (interfragment) interactions. Deformation energies are divided into charge transfer and redistribution terms and their relative roles are analyzed. A number of systems are compared against the fuzziness of different density decompositions. The results consistently show that fuzzy partitions tend to give low atomic net charges and enhanced covalency, while exhaustive partitions generate larger net charges and smaller covalencies, across a wide range of bonding regimes.

Journal Article↗

PubMed2006

Binding energies of first row diatomics in the light of the interacting quantum atoms approach.

Binding energies of first row diatomics are revisited within the interacting quantum atoms (IQA) approach. This is a formalism in chemical bonding theory based upon the quantum theory of atoms in molecules. It is characterized by the preservation of the energetic identity of atoms within molecules. Quantum mechanically computed binding energies are recovered in IQA as a sum of small atomic deformation energies and large pairwise interaction terms. We show how this partition responds faithfully to chemical intuition, and how the different evolution of deformations and interactions accounts in a unified manner for the subtle variations of the binding energy of these molecules.

Journal Article↗

PubMed2006

The nature of the hydrogen bond: a synthesis from the interacting quantum atoms picture.

The interacting quantum atoms approach [IQA, as presented by Blanco et al., J. Chem. Theory Comput. 1, 1096 (2005)] is applied to standard hydrogen bonded dimers. IQA is an interpretation tool based on a real space energy decomposition scheme fully consistent with the quantum theory of atoms in molecules. It provides a partition of every physical term present in the Hamiltonian into atomic and interatomic contributions. The procedure is orbital-free and self-contained, needing neither external references nor artificial intermediate states. Binding is the result of a competition between the destabilizing deformations suffered by the interacting fragments upon interaction and the stabilizing interaction energy itself. According to IQA, there is no incompatibility between the prevalent electrostatic image of hydrogen bonded systems and that favoring important covalent contributions. Depending on how we gather the different energetic terms, we may recover electrostatic or covalent pictures from the same underlying quantum mechanical description. Our results show that the nonclassical contributions to hydrogen bonding are spatially localized, involving only the H atom and its two nearest neighbors. IQA is well suited as a comparative tool. Its thin energetic decomposition allows us to recover exactly (or to a very good approximation) the quantities of the most widely used energy decomposition schemes. Such a comparison sheds light on the virtues and faults of the different methods and on the origin of the 50 years old debate regarding the covalent/electrostatic nature of the hydrogen bond.

Journal Article↗

PubMed2006

First principles study of neutral and anionic (medium-size) aluminum nitride clusters: AlnNn, n=7-16.

We report the results of a theoretical study of AlnNn (n=7-16) clusters that is based on density functional theory. We will focus on the evolution of structural and electronic properties with the cluster size in the stoichiometric AlN clusters considered. The results reveal that the structural and electronic properties tend to evolve toward their respective bulk limits. The rate of evolution is, however, slow due to the hollow globular shape exhibited by the clusters, which introduces large surface effects that dominate the properties studied. We will also discuss the changes induced upon addition of an extra electron to the respective neutral clusters.

Journal Article↗

PubMed2005

Evolution of the properties of Al(n)N(n) clusters with size.

A global optimization of stoichiometric (AlN)(n) clusters (n = 1-25, 30, 35, ..., 95, 100) has been performed using the basin-hopping (BH) method and describing the interactions with simple and yet realistic interatomic potentials. The results for the smaller isomers agree with those of previous electronic structure calculations, thus validating the present scheme. The lowest-energy isomers found can be classified in three different categories according to their structural motifs: (i) small clusters (n = 2-5), with planar ring structures and 2-fold coordination, (ii) medium clusters (n = 6-40), where a competition between stacked rings and globular-like empty cages exists, and (iii) large clusters (n > 40), large enough to mix different elements of the previous stage. All the atoms in small and medium-sized clusters are in the surface, while large clusters start to display interior atoms. Large clusters display a competition between tetrahedral and octahedral-like features: the former lead to a lower energy interior in the cluster, while the latter allow for surface terminations with a lower energy. All of the properties studied present different regimes according to the above classification. It is of particular interest that the local properties of the interior atoms do converge to the bulk limit. The isomers with n = 6 and 12 are specially stable with respect to the gain or loss of AlN molecules.

Journal Article↗

PubMed2005

Global optimization of ionic Mg(n)F(2n) (n=1-30) clusters.

The global optimization basin-hopping (BH) method has been used to locate the global minima (GM) of Mg(n)F(2n) (n=1-30) clusters using a Born-Mayer-type potential. Some of the GM were particularly difficult to find, requiring more than 1.5 x 10(4) BH steps. We have found that both the binding energy per MgF2 unit and the effective volume of the GM isomers increase almost linearly with n, and that cluster symmetry decreases with cluster size. The data derived from the BH runs reveal a growing density of local minima just above the GM as n increases. Despite this, the attraction basin around each GM is relatively large, since after all their atomic coordinates are randomly displaced by values as high as 2.0 bohrs, the perturbed structures, upon reoptimization, relax back to the GM in more than 50% of the cases (except for n=10 and 11). The relative stabilities derived from energy second differences suggest that n=8,10,13,15, and 20 are probably the magic numbers for these systems. Mass spectrum experiments would be very useful to clarify this issue.

Algorithms↗

PubMed2005

Two-electron integrations in the quantum theory of atoms in molecules with correlated wave functions.

A recent method proposed to compute two-electron integrals over arbitrary regions of space [Martin Pendas, A. et al., J Chem Phys 2004, 120, 4581] is extended to deal with correlated wave functions. To that end, we use a monadic factorization of the second-order reduced density matrix originally proposed by E. R. Davidson [Chem Phys Lett 1995, 246, 209] that achieves a full separation of the interelectronic components into one-electron terms. The final computational effort is equivalent to that found in the integration of a one determinant wave function with as many orbitals as occupied functions in the correlated expansion. Similar strategies to extract the exchange and self-interaction contributions from the two-electron repulsion are also discussed, and several numerical results obtained in a few test systems are summarized.

Journal Article↗

PubMed2004

Two-electron integrations in the quantum theory of atoms in molecules.

A method to compute two-electron integrals over arbitrary regions of space is introduced and particularized to the basins appearing in the quantum theory of atoms in molecules. The procedure generalizes the conventional multipolar approach to account for overlapping densities. We show that the approach is always convergent and computationally efficient, scaling as N(4) in the worst, two-center case. Several numerical results supporting our claims are also presented.

Journal Article↗

PubMed1999

Analysis of cell surface properties using derivatized agarose beads.

An assay has been developed to analyse cell surface properties using agarose beads derivatized with amino acids, sugars, proteins, and other molecules. The assay is simple and rapid and is useful to identify new cell surface markers. Various species and strains of yeast, paramecium, and Euglena were tested for their ability to bind to over 100 types of derivatized beads. A variety of specificity studies were performed in order to understand the nature of cell-bead binding. Our results indicate that cell-bead binding is often specific enough to distinguish between configurational isomers and spacer sizes and can be blocked by addition of specific molecules to the incubation medium. In some cases, different species or strains differed only by their binding to a single bead type. This simple and rapid assay may help to uncover new cell surface receptors and may lead to the development of clinically useful compounds for therapeutic applications.

Amino Acids↗

PubMed1995