Publicaciones 2011-2020

@article{orellana2017palmitic,
title = {Palmitic Acid and Hexadecylamine Molecules Assdsorbed on Titania Surface in Hybrid Composites. Effect of Surfactants Using Density Functional Theory},
author = { C. Orellana and F. Mendizabal and G. Gonz\'{a}lez and S. Miranda-Rojas and L. Barrientos-Poblete},
url = {/brokenurl#<Go to ISI>://WOS:000401679900007},
doi = {10.1016/j.comptc.2017.04.006},
issn = {2210-271x},
year = {2017},
date = {2017-01-01},
journal = {Computational and Theoretical Chemistry},
volume = {1110},
pages = {50-59},
publisher = {2017 Elsevier B.V.},
abstract = {A complete theoretical characterization of the factors involved in the stabilization of hybrid laminar composites is reported, with the purpose of understanding the main interactions involved in the formation of these types of systems. The models were built using two different surfactants: hexadecylamine (HDA) and palmitic acid (PAc), on a cluster of titania (TiO2) which represents its anatase crystalline phase. We explored the relevance of the titania-surfactant and surfactant-surfactant interactions, and of the protonation state of the palmitic acid in the stabilization of the hybrid laminar composites. The results were rationalized using energy decomposition analysis (EDA) and the non-covalent interaction index (NIC). The interaction energies between HDA and the TiO2 surface without the contribution of the dispersion forces were -25 kcal/mol and -29 kcal/mol for the (1 0 0) and (1 01) surfaces, respectively. These results suggest the formation of a donor-acceptor bond between HDA-TiO2 allowing its stabilization. On the other hand, the interaction energy between PAc and the TiO2 (1 0 1) surface was about -45 kcal/mol without the dispersion term. Thus, the PAc-TiO2 model has a higher covalent character than the HDA-TiO2 interaction, as confirmed by the energy decomposition analyses. The results suggest new hybrid laminar composites which are better when carboxylic acid was used instead of amines. Therefore, the use of surfactants with the carboxyl functional group yielded more stable TiO2 hybrid composites. The interaction energy between surfactant chains was about -13 kcal/mol, confirming the importance of dispersion forces in the stabilization of these types of systems. The study of systems with palmitic acid was complemented by building some anionic models to show the importance of acid protons in those systems. However, when the acidic hydrogens were removed, the interaction energy between the PAc molecules considering the dispersion correction increased to 45 kcal/mol, with a highly repulsive character. These results suggest that the acid hydrogens of the PAc surfactants play a fundamental role in terms of correctly representing the carboxylic acid-TiO2 interface and the stabilization of the laminar hybrid composites.},
keywords = {basis-sets, bsse, calculations, catalysis, clusters, compounds, dft dft, dioxide dispersion enzymatic hexadecylamine, hydrogen-bonds, interactions, laminar n-body noncovalent palmitic photocatalysis properties, sensitized solar-cells, spectroscopic strong term, tio2, titanium},
pubstate = {published},
tppubtype = {article}
}

@article{hugo2017functional,
title = {Functional Roles of T3.37 and S5.46 in the Activation Mechanism of the Dopamine D1 Receptor},
author = { E.A. Hugo and B.K. Cassels and A. Fierro},
url = {/brokenurl#<Go to ISI>://WOS:000399406500014},
doi = {10.1007/s00894-017-3313-0},
issn = {1610-2940},
year = {2017},
date = {2017-01-01},
journal = {Journal of Molecular Modeling},
volume = {23},
number = {4},
abstract = {The activation mechanism of dopamine receptors is unknown. The amino acids S5.42, S5.43, and S5.46 located in helix 5 appear to be crucial, but their specific roles in receptor activation have not been studied. We modeled the D1 dopamine receptor using the crystal structures of the D3 dopamine and beta 2 adrenergic receptors. Molecular dynamics simulations show that the interaction of dopamine with the D1 receptor leads to the formation of a hydrogen-bond network with its catechol group and helices 3, 5, and 6, including water molecules. The para hydroxyl group of dopamine binds directly to S5.42 and N6.55, the latter also interacting with S5.43. Unexpectedly, S5.46 does not interact directly with the catechol; instead, it interacts through a water molecule with S5.42 and directly with T3.37. The formation of this hydrogen-bond network, part of which was previously observed in docking studies with dopamine agonists, triggers the opening of the E6.30-R3.60 ionic lock associated with the activation of GPCRs. These changes do not occur in the unbonded (apo) receptor or when it is in a complex with the antagonist 3-methoxy- 5,6,7,8,9,14-hexahydrodibenz[d, g]azecine. Our results provide valuable insight into the T3.37-S5.46-water-S5.43-ligand interaction, which may be crucial to the activation of the D1 dopamine receptor and should be considered during the design of novel agonists.},
keywords = {crystal-structure, d-1, d1 dopamine dopamine, dynamics, identification, interactions, models, molecular pharmacophore, receptor, recognition residues, s5.46, serine structures},
pubstate = {published},
tppubtype = {article}
}

@article{RN244,
title = {Molecular Dynamics Simulation of Halogen Bonding Mimics Experimental Data for Cathepsin L Inhibition},
author = { C. Celis-Barros and L. Saavedra-Rivas and J.C. Salgado and B.K. Cassels and G. Zapata-Torres},
url = {/brokenurl#<Go to ISI>://WOS:000346913200004},
doi = {10.1007/s10822-014-9802-7},
issn = {0920-654x},
year = {2015},
date = {2015-01-01},
journal = {Journal of Computer-Aided Molecular Design},
volume = {29},
number = {1},
pages = {37-46},
abstract = {A MD simulation protocol was developed to model halogen bonding in protein-ligand complexes by inclusion of a charged extra point to represent the anisotropic distribution of charge on the halogen atom. This protocol was then used to simulate the interactions of cathepsin L with a series of halogenated and non-halogenated inhibitors. Our results show that chloro, bromo and iodo derivatives have progressively narrower distributions of calculated geometries, which reflects the order of affinity I > Br > Cl, in agreement with the IC50 values. Graphs for the Cl, Br and I analogs show stable interactions between the halogen atom and the Gly61 carbonyl oxygen of the enzyme. The halogen-oxygen distance is close to or less than the sum of the van der Waals radii; the C-X center dot center dot center dot O angle is about 170A degrees; and the X center dot center dot center dot O=C angle approaches 120A degrees, as expected for halogen bond formation. In the case of the iodo-substituted analogs, these effects are enhanced by introduction of a fluorine atom on the inhibitors' halogen-bonding phenyl ring, indicating that the electron withdrawing group enlarges the sigma-hole, resulting in improved halogen bonding properties.},
keywords = {atherosclerosis, bonding, bromine cathepsin cathepsins, cysteine design, discovery, disease, drug force-field, halogen halogenated inhibitors, interactions, l, md optimization, protein-ligand sigma-hole, simulation},
pubstate = {published},
tppubtype = {article}
}

@article{castro2013kinetic,
title = {Kinetic and Theoretical Study on Nucleofugality in the Phenolysis of 3-Nitrophenyl and 4-Nitrophenyl 4-Cyanophenyl Thionocarbonates},
author = { E.A. Castro and A. Canete and P.R. Campodonico and M. Cepeda and P. Pavez and R. Contreras and J.G. Santos},
url = {/brokenurl#<Go to ISI>://WOS:000319332600025},
doi = {10.1016/j.cplett.2013.04.002},
issn = {0009-2614},
year = {2013},
date = {2013-01-01},
journal = {Chemical Physics Letters},
volume = {572},
pages = {130-135},
publisher = {2013 Elsevier B.V.},
abstract = {The phenolysis of 3-nitrophenyl 4-cyanophenyl thionocarbonate (1) and 4-nitrophenyl 4-cyanophenyl thionocarbonate (2) are subjected to a kinetic investigation in order to evaluate the nucleofugality of the corresponding leaving groups. For the reaction of 2 only 4-nitrophenoxide is obtained as leaving group. For the reaction of 1 the nucleofugality ratio 3-nitrophenoxide/4-cyanophenoxide is 1/3 from the corresponding T intermediate. Theoretical calculations confirm the experimental results. From these results it can be concluded that the non-leaving group affects the nucleofugality ratio.},
keywords = {aminolysis, carbonates, electronic elimination, ester geminal groups, interactions, leaving mechanism, quality, reactivity, scale},
pubstate = {published},
tppubtype = {article}
}

@article{RN142,
title = {Theoretical Study of Complexes of the Type [Pt-3(M-L)(3)(L ')(3)]-X (L=Co,So2,Cnh; L '=Ph3,Cnh; X=Tl+, Hg-0, Mph3+ (M = Cu, Au, Ag))},
author = { F. Mendizabal and D. Donoso and R. Salazar},
url = {/brokenurl#<Go to ISI>://WOS:000331236900014},
issn = {0717-9707},
year = {2013},
date = {2013-01-01},
journal = {Journal of the Chilean Chemical Society},
volume = {58},
number = {1},
pages = {1562-1570},
abstract = {The interaction between the [Pt-3(mu-L)(3)(L')(3)] cluster (L = CO, SO2, CNH; L' = PH3, CNH) and a series of fragments X (Tl+, Hg(0), AuPH3+, CuPH3+ and AgPH3+) was studied using ab initio methodology. The calculations suggest that the complexes formed are stable. We have studied these complexes at the HF, MP2, B3LYP and PBE levels of theory. The magnitude of the interaction energies and Pt-3-MPH3+ distances indicate a substantial covalent character of the bond. On the other hand, in [Pt-3(mu-L)(3)(L')(3)]-X (Tl+ and Hg) the energy magnitudes are in the order of metallophilic interaction, which indicates that the dispersion and ionic terms are found as the main contribution to stability. These results have been confirmed by orbital diagrams. In addition, the Fukui index of electrophilic attack and electrophilicity index on the [Pt-3(mu-L)(3)(L')(3)] clusters were used to explore possible sites that may play a role in chemical reactivity.},
keywords = {approximation, chemical-reactivity, chemistry cluster clusters, complexes, crystal-structure, electronegativity, electrophilicity index, interactions, metallic platinum pseudopotentials, reactivity, units},
pubstate = {published},
tppubtype = {article}
}

@article{RN6c,
title = {Basicity of Bisperhalophenyl Aurates toward Closed-Shell Metal Ions: Metallophilicity and Additional Interactions},
author = { J.M. Lopez-De-Luzuriaga and M. Monge and M.E. Olmos and M. Rodriguez-Castillo and A. Laguna and F. Mendizabal},
url = {/brokenurl#<Go to ISI>://WOS:000290572300031},
doi = {10.1007/s00214-011-0902-3},
issn = {1432-881x},
year = {2011},
date = {2011-01-01},
journal = {Theoretical Chemistry Accounts},
volume = {129},
number = {3-5},
pages = {593-602},
abstract = {The interaction of bisperhalophenyl aurates [AuR2](-) (R = C6F5, C6F3Cl2, and C6Cl5) with the closed-shell Ag+, Cu+, and Tl+ ions has been studied theoretically and compared with the experimentally known X-ray diffraction crystal structures. Initially, the aurates have been fully optimized at MP2 level of theory in a D (2h) symmetry. The analysis of the basicity of the three aurates [AuR2](-) (R = C6F5, C6F3Cl2 and C6Cl5) against Ag+ ions in a C (2v) symmetry has been calculated in point-by-point bsse-corrected interaction energy analysis at HF and MP2 levels of theory. Taking into account the experimental observation of additional interactions between the heterometals and C (ipso) atoms at the perhalophenyl rings or halogen atoms at the ortho position of the perhalophenyl rings, dinuclear models of the type [AuR2](-)center dot center dot center dot Ag+ (R = C6Cl5, and C6F5); [AuR2](-)center dot center dot center dot Cu+ (R = C6F5, and C6Cl5) and [AuR2](-)center dot center dot center dot Tl+ (R = C6F5, and C6Cl5) with a C (2v) , C (2) , and C (s) symmetries have been optimized at DFT-B3LYP level. The interaction energies have been computed through bsse-corrected single point HF and MP2 calculations. The energy stabilization provided and the heterometal preference have been analyzed and compared with the experimental results.},
keywords = {au, chemistry, complexes copper, gold, interactions, metal-metal silver, thallium, theoretical},
pubstate = {published},
tppubtype = {article}
}