Biomedical subjects

Patricia Guadarrama

Publications and source records attributed to Patricia Guadarrama.

4 recordsLinked to original sources

PubMed2006

Oligothiophene catenanes and knots: a theoretical study.

Oligothiophene [2]catenanes and knots containing up to 28 thiophene units have been studied at the BHandHLYP/3-21G level of theory. Small knots (less than 22 thiophene units) and [2]catenanes (less than 18 thiophene units) are strained molecules. Larger knots and [2]catenanes are almost strain-free. [2]Catenanes and knots having less than 18 and 24 units, respectively, show transversal electronic coupling destroying one-dimensionality of molecules reflecting in smaller band gaps compared to larger knots and catenanes. Ionization potentials of knots and catenanes are always higher compared to that of lineal oligomers due to less effective conjugation. Polaron formation in catenanes is delocalized only over one ring, leaving another intact. In the case of a knot containing 22 thiophene units, estimated polaron delocalization is 8 to 9 repeating units.

Journal Article↗

PubMed2005

Interactions in pseudorotoxanes based on crown ether-secondary ammonium motifs. A theoretical study.

A theoretical analysis of the nature of the interactions in dibenzo[24]crown-8 (DB24C8)-n-dibutylammonium (DBM)--pseudorotaxane complex at the MP2 and DFT levels shows that the main contribution to the binding energy is the electrostatic interaction with moderate (20-25%) correlation stabilization. The total binding energy in the DB24C8-DBM complex represents a sum of the binding energies of two NH-O and one CH-O hydrogen bonds and the latter constitutes about 25% of the total interaction energy, giving the total binding energy of -41.2 kcal mol(-1) at the BHandHLYP/6-311 + + G** level. Deprotonation of the DB24C8-DBM complex reduces the binding energy by some 50 kcal mol(-1), giving metastable complexes DB24C8-DBA-1 or DB24C8-DBA-2, which will dissociate to give free crown ether and n-dibutylamine because of the strong exchange repulsion that prevails in neutral complexes.

Crown Ethers↗

PubMed2004

Macrocyclic vs. dendrimeric effect. A DFT study.

Macrocycles up to 15 members with different heteroatoms (N, O, and S) and dendrimeric functionalized branches were assembled, resulting in unique "collective" supramolecular hosts with several active sites for transition metal ions complexation. The nature of the interactions between these kinds of systems and metal ions of the first transition series (Fe, Ni, Cu, Zn) was evaluated by calculations of the binding energies at the B3LYP/LACVP* level of theory, resulting in a preference of metal ions for macrocyclic cavity in terms of complexation; however, there is a favorable contribution in energy due to the cooperative effect of dendrimeric branches (DBs) in the inclusion process by means of long-range interactions between metal ions and the heteroatoms present in DBs. According to calculated binding energies, even when the complexation in the middle of DBs appears as a less favored situation, still competes with the complexation occurred in several known macrocycles traditionally used in the formation of inclusion complexes. The capability of macrocycles as host entities is related to some criteria like: (1) the compatibility in orbital symmetry between host and guest molecules; (2) the cavity dimensions and the negative charge inside; and (3) the hardness-softness affinity between host and guest molecules. When DBs are included in host systems, their flexibility seems to be very important, in addition to localized negative charge, which permits the occurrence of long-range interactions.

Journal Article↗

PubMed2003

Cyclen substitution with urea-containing dendrimeric branches. Theoretical study considering the concept of collectivity.

Equilibrium structures of novel dendrimeric compounds consisting of 1,4,7,10-tetraazacyclododecane (cyclen) mono- to tetra-substituted with four different dendrimeric branches have been studied. It has been shown using molecular dynamics (MD) that, even in the presence of the macrocycle cyclen, the most stable conformations are those with a globular shape due to close contact interactions between poly-functional branches. No collapse of cyclen occurred, making this cavity available for metal complexation. Terminal branches A=NHCOOtBu, B=OSi(Me)2tBu, C=Imidazole and D=CN have different molecular volumes in the decreasing order: B>A>C>D. This conclusion is in accord with the long range interaction energies, showing that the larger the volume the less the steric hindrance. Considering these energy values, the stability of the systems follows exactly the same tendency as observed for the molecular volume. More polar groups like A=NHCOOtBu and D=CN impart extra stability due to long range interactions between atoms separated by exactly three chemical bonds. The negative charge inside the cyclen cavity increases with the volume of the branches. Besides cyclen, urea groups located at the middle of the branches represent another independent point of negative charge for eventual interaction with small molecules. These compounds show a sum of small contributions of the functionalities in a collective fashion.

Computer-Aided Design↗