Publicaciones 2011-2020

@article{RN394,
title = {Unraveling the Nature of the Catalytic Power of Fluoroacetate Dehalogenase},
author = { S. Miranda-Rojas and I. Fernandez and J. Kastner and A. Toro-Labbe and F. Mendizabal},
url = {/brokenurl#<Go to ISI>://WOS:000426844600026},
doi = {10.1002/cctc.201701517},
issn = {1867-3880},
year = {2018},
date = {2018-01-01},
journal = {Chemcatchem},
volume = {10},
number = {5},
pages = {1052-1063},
abstract = {Fluoroacetate dehalogenase is able to cleavage a carbon-fluoride bond, the strongest carbon-halogen bond in nature, in a process initiated by a S(N)2 reaction. The role of the enzyme machinery and particularly of the halogen pocket in the S(N)2 reaction is thoroughly explored by using state-of-the-art computational tools. A comparison between the non-catalyzed versus enzyme-catalyzed reaction, as well as with a mutant of the enzyme (Tyr219Phe), is presented. The energy barrier changes are rationalized by means of reaction force analysis and the activation strain model coupled with energy decomposition analysis. The catalysis is in part caused by the reduction of structural work from bringing the reactant species towards the proper reaction orientation, and the reduction of the electrostatic repulsion between the nucleophile and the substrate, which are both negatively charged. In addition, catalysis is also driven by an important reduction of the electronic reorganization processes during the reaction, where Tyr from the halogen pocket acts as a charge acceptor from the S(N)2 reaction axis therefore reducing the electronic steric repulsion between the reacting parts.},
keywords = {approach, bond, carbon-fluorine catalysis, chemical cluster decomposition density-functional displacement, dynamics, energy enzyme force, mechanism model, molecular-orbital qm/mm, transition-state},
pubstate = {published},
tppubtype = {article}
}

@article{RN419,
title = {How Meaningful Is the Halogen Bonding in 1-Ethyl-3-Methyl Imidazolium-Based Ionic Liquids for Co2 Capture?},
author = { L. Lodeiro and R. Contreras and R. Ormazabal-Toledo},
url = {/brokenurl#<Go to ISI>://WOS:000442437700011},
doi = {10.1021/acs.jpcb.8b04990},
issn = {1520-6106},
year = {2018},
date = {2018-01-01},
journal = {Journal of Physical Chemistry B},
volume = {122},
number = {32},
pages = {7907-7914},
abstract = {We report on several parameters that can be used to describe the 1-ethyl-3-methyl-4,5-(X-2)imidazolium cations (where X = H, Br, and I) within the Canongia-Lopez and Padua Force Field (CL&P) framework. Geometrical parameters like intramolecular distances and radial distribution functions are close to the experimental structure. Density values obtained with our force field are within the expected ones from CL&P calculations in related systems. This information is used to simulate through molecular dynamics the solubilization of CO2 by these ILs. For pure ILs, the addition of halides in position 4 and 5 promotes an enhanced hydrogen bond interaction at position 2 with the oxygen atoms in the anion. It is found that CO2 should be in the interstices of the anion-cation 3D network with longer distances than those found in other reports at ab initio levels, suggesting that halogen bond, if present, may be not the driving force interaction in these systems. Therefore, it seems that CO2 interacts linearly via an oxygen atom with the cation and with the anion through a pi-stacking or hydrogen-bonded fashions. Solvation enthalpies compare well with the experimental data, thereby suggesting that halogenated ILs dissolve more efficiently in CO2 than C(2)C(1)Im(+) derivatives. This result suggests that halogenated ILs can be considered as reliable candidates for CO2 capture.},
keywords = {atmospheric carbon-dioxide, co2, conversion, dynamics, field, hydrogen-bonds, mechanism molecular-force reactivity, solubility, solvents},
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{RN374,
title = {Trend and Recovery of the Total Ozone Column in South America and Antarctica},
author = { R. Toro and C. Araya and F. Labra and L. Morales and R.G.E. Morales and M.A. Leiva},
url = {/brokenurl#<Go to ISI>://WOS:000415579000006},
doi = {10.1007/s00382-017-3540-1},
issn = {0930-7575},
year = {2017},
date = {2017-01-01},
journal = {Climate Dynamics},
volume = {49},
number = {11-12},
pages = {3735-3752},
abstract = {South America is one of the most vulnerable areas to stratospheric ozone depletion; consequently, an increased amount of UV radiation reaches the Earth's surface in this region. In this study, we analyzed the long-term trend in the total ozone column (TOC) over the southern part of the South American continent from 1980 to 2009. The database used was obtained by combining several satellite measurements of the TOC on a 1A degrees (latitude) x 1.25A degrees (longitude) grid. Analysis of the long-term trend was performed by applying the Theil-Sen estimator and the Mann-Kendall significance test to the deseasonalized time series. The long-term trend was also analyzed over several highly populated urban zones in the study area. Finally, multiple linear regression (MLR) modeling was used to identify and quantify the drivers of interannual variability in the TOC over the study area with a pixel-by-pixel approach. The results showed a decrease in the TOC ranging from -0.3 to -4% dec(-1) from 1980 to 2009. On a decadal timescale, there is significant variability in this trend, and a decrease of more than -10% dec(-1) was found at high latitudes (1980-1989). However, the trends obtained over much of the study area were not statistically significant. Considering the period from 1980 to 1995, we found a decrease in the TOC of -2.0 +/- 0.6% dec(-1) at latitudes below 40A degrees S and -6.9 +/- 2.0% dec(-1) at latitudes above 40A degrees S, for a 99.9% confidence level over most of the study area. Analysis of the period from 1996 to 2009 showed a statistically significant increase of 2.3 +/- 0.1% dec(-1) at high latitudes (> 60A degrees S), confirming the initial TOC recovery in the Antarctic. Despite evidence for initial recovery of the TOC in some parts of the study area between 1996 and 2009, the long-term increase from September to November is not yet statistically significant. In addition, large parts of the study area and most of the urban areas continue to show a decreasing trend in the TOC. The MLR results show that at high latitudes, the main driver of interannual variability in the TOC is the total effective amount of halogens, followed by the eddy heat flux.},
keywords = {analysis, arosa atmospheric chemistry, column, cycle, decadal depletion, dynamics, environmental chemistry, estimator, events, extratropical extreme interannual linear long-term multiple oscillation, ozone ozone, punta-arenas, quasi-biennial regression, sunspot theil-sen total trend variability, variation},
pubstate = {published},
tppubtype = {article}
}

@article{RN261,
title = {Raman and Surface Enhanced Raman Signals of the Sensor 1-(4-Mercaptophenyl)-2,4,6-Triphenylpyridinium Perchlorate},
author = { F. Celis and M. Campos-Vallette and J.C. Vega and J.S. Gomez-Jeria and C. Aliaga},
url = {/brokenurl#<Go to ISI>://WOS:000361545700018},
doi = {10.4067/S0717-97072015000200018},
issn = {0717-9707},
year = {2015},
date = {2015-01-01},
journal = {Journal of the Chilean Chemical Society},
volume = {60},
number = {2},
pages = {2944-2948},
abstract = {The sensor 1-(4-mercaptophenyl)-2,4,6-triphenylpyridinium perchlorate compound was vibrationally characterized using Raman and the Surface-Enhanced Raman techniques, SERS and Shell-Isolated Nanoparticles-Enhanced Raman Spectroscopy (SHINERS). The Raman spectrum was analyzed and the band assignment was supported using DFT data at the B3LYP/6-31G(d) level. SERS data allowed infer about the orientation of the analyte on the naked Ag surface. EHT calculations for an Ag/analyte model represent well the SERS spectrum supporting the Ag-S bond formation. The SHINERS spectrum was obtained by using Ag
@SiO2 nanoparticles prepared at two different time of the SiO2 coating process. The most intense SHINERS spectral signals of the compound (100 nM) were obtained after 20 minutes of the Ag
@SiO2 formation. No charge-transfer was concluded from the SHINERS experiments.},
keywords = {density dft dyes, dynamics, eht halochromism, hydrocarbons, perchlorate, raman, scattering, sers, shiners, silver, solvent spectroscopy},
pubstate = {published},
tppubtype = {article}
}

@article{RN213,
title = {Thermodynamics and (Hnmr)-H-2 Study on the Insertion of Small Quinones into a Discotic Nematic Lyotropic Liquid Crystal},
author = { V.E. Bahamonde-Padilla and J.J. Lopez-Cascales and R. Araya-Maturana and M. Martinez-Cifuentes and B. Weiss-Lopez},
url = {/brokenurl#<Go to ISI>://WOS:000335515900018},
doi = {10.1002/cphc.201301146},
issn = {1439-4235},
year = {2014},
date = {2014-01-01},
journal = {Chemphyschem},
volume = {15},
number = {7},
pages = {1422-1431},
abstract = {A detailed description of the distribution, interaction, and dynamics of molecules with biological activity dissolved in a hydrophobic bilayer, a simple model of a biological membrane, provides valuable information for a better understanding of drug functioning, which can be very useful in drug design. Here we present an H-2 NMR and molecular dynamics study on the insertion, distribution, interactions, and thermodynamics of two biologically active molecules, 9,10-dihydroxy-4,4-dimethyl-1,4,5,8-tetrahydroanthracen-1-one (HQ), with anticancer activity, and 4,4-dimethyl-1,4,5,8,9,10-hexahydroanthracen-1,9,10-trione (Q) a fungicide, dissolved in a nematic discotic lyotropic liquid crystal (ndllc) composed of sodium dodecylsulphate (SDS), decanol (DecOH) and Na2SO4 in water. H-2 NMR quadrupole splittings ((Q)) and longitudinal relaxation times (T-1) from HQ-d(6), Q-d(4), DecOH--d(2), partially deuterated water, and SDS-d(25) were measured and several molecular dynamics trajectories were also calculated. In particular, G, H, and S profiles for the process of both molecules crossing the bilayer were estimated. It was evidenced that the insertion of both molecules into the aggregate is a spontaneous process, and the molecules are mainly distributed in the internal side of the interface. Addition of HQ or Q decreased the mobility of all aggregate components, but this effect was more pronounced for HQ. The rotational correlation time of Q allowed an estimate of 5.3 cP for the microviscosity inside the ndllc aggregate, in the order of previously measured values in similar environments. Both guest molecules display similar free-energy profiles for the process of crossing the bilayer, with a calculated barrier height of 25 and 36 kJmol(-1) for HQ and Q, respectively.},
keywords = {aqueous-solution, crystals, derivatives, dynamics, ewald, force-field, free-energy, lipid-bilayer, liquid membrane, mesh micelle microviscosity, molecular molecular-dynamics nmr particle quinones, resonance, simulations, spectroscopy},
pubstate = {published},
tppubtype = {article}
}

@article{RN193,
title = {A Coumarinylaldoxime as a Specific Sensor for Cu2+ and Its Biological Application},
author = { O. Garcia-Beltran and B.K. Cassels and N. Mena and M. Nunez and O. Yanez and J. Caballero},
url = {/brokenurl#<Go to ISI>://WOS:000330604500023},
doi = {10.1016/j.tetlet.2013.12.033},
issn = {0040-4039},
year = {2014},
date = {2014-01-01},
journal = {Tetrahedron Letters},
volume = {55},
number = {4},
pages = {873-876},
publisher = {2013 Elsevier Ltd.},
abstract = {In this Letter we present a new probe, (E)-7-(diethylamino)-2-oxo-2H-chromene-3-carbaldehyde oxime (JB), which can detect Cu2+ ions in HEPES buffer under physiological conditions. Benesi-Hildebrand and Job plots demonstrate that the stoichiometry of the Cu2+ complex formed is 2:1. Possible interference with other analytes was examined, and the decrease of the fluorescence of JB at 510 nm when it reacts with Cu2+ was shown to be highly selective. This probe accumulates in the plasmalemma of human neuroblastoma SH-SY5Y cells. Molecular dynamics (MD) simulations revealed thatJB interacts with the lipid bilayer at the level of the glycerol moieties.},
keywords = {bilayer, copper, coumarin cu2+-selectivity, derivative, design, dynamics, fluorescent lipid membranes molecular probe},
pubstate = {published},
tppubtype = {article}
}

@article{RN192,
title = {Synthesis of Coumarin Derivatives as Fluorescent Probes for Membrane and Cell Dynamics Studies},
author = { O. Garcia-Beltran and O. Yanez and J. Caballero and A. Gald\'{a}mez and N. Mena and M. Nunez and B.K. Cassels},
url = {/brokenurl#<Go to ISI>://WOS:000335487400009},
doi = {10.1016/j.ejmech.2014.02.016},
issn = {0223-5234},
year = {2014},
date = {2014-01-01},
journal = {European Journal of Medicinal Chemistry},
volume = {76},
pages = {79-86},
publisher = {2014 Elsevier Masson SAS.},
abstract = {Three coumarin-derived fluorescent probes, 3-acetyl-7-[(6-bromohexyl)oxy]-2H-chromen-2-one (FM1), 7-[(6-bromohexyl)oxy]-4-methyl-2H-chromen-2-one (FM2) and ethyl 2-7-[(6-bromohexyl)oxy]-2-oxo-2H-chromen-4-ylacetate (FM3), are described, with their photophysical constants. The compounds were tested in preliminary studies employing epifluorescence microscopy demonstrating that they allow the imaging of human neuroblastoma SH-SY5Y cell membranes. The structure of FM3 was confirmed by X-ray crystallographic analysis. Molecular dynamics (MD) simulations were used to characterize the localization and interactions of the studied compounds with a lipid bilayer model of 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC).},
keywords = {biological-membranes, carboxylic-acids, cell coumarins, crystal-structure, decarboxylation depth, dynamics, energy-transfer, hydrogen-bond, membranes, model, molecular molecular-dynamics, probes, proteins, resonance},
pubstate = {published},
tppubtype = {article}
}

@article{RN125,
title = {Design, Synthesis and Cellular Dynamics Studies in Membranes of a New Coumarin-Based "Turn-Off" Fluorescent Probe Selective for Fe2+},
author = { O. Garcia-Beltran and N. Mena and O. Yanez and J. Caballero and V. Vargas and M. Nunez and B.K. Cassels},
url = {/brokenurl#<Go to ISI>://WOS:000325121800007},
doi = {10.1016/j.ejmech.2013.06.022},
issn = {0223-5234},
year = {2013},
date = {2013-01-01},
journal = {European Journal of Medicinal Chemistry},
volume = {67},
pages = {60-63},
publisher = {2013 Elsevier Masson SAS.},
abstract = {A new coumarin-based 'turn-off' fluorescent probe, 7-(diethylamino)-N-(1,3-dihydroxy-2-(hydroxymethyl)propan-2-yl)-2-oxo-2H-chromene-3-carboxamide (AGD) was synthesized. This compound is highly selective for ferrous ions (Fe2+) and can reversibly detect them in aqueous medium. The probe localizes to the cell membrane in living cells, where it can detect changes in Fe2+ concentration. Molecular dynamics (MD) simulations indicate that AGD interacts with the lipid bilayer at the level of the glycerol moieties.},
keywords = {cells, chelatable chelators, chemosensor, deficiency, dynamics, fe2+ fe3+ fluorescent ion, iron, labile molecular probes, sensor, turn-off},
pubstate = {published},
tppubtype = {article}
}

@article{RN29d,
title = {Influence of Tio2 on Prebiotic Thermal Synthesis of the Gly-Gln Polymer},
author = { P. Leyton and R. Saladino and C. Crestini and M. Campos-Vallette and C. Paipa and A. Berrios and S. Fuentes and R.A. Zarate},
url = {/brokenurl#<Go to ISI>://WOS:000304150300004},
doi = {10.1007/s00726-011-0939-6},
issn = {0939-4451},
year = {2012},
date = {2012-01-01},
journal = {Amino Acids},
volume = {42},
number = {6},
pages = {2079-2088},
abstract = {The role of the titanium dioxide (rutile and anatase) with and without room light on the thermal synthesis of the glycine--glutamine (Gly-Gln) polymer is described. The efficiency in percentage of polymerization with room light was increased in 6% in the presence of rutile and in 23% in the presence of anatase. The thermal synthesis in the molten state was carried out in the absence and presence of both oxides. In all cases, the vibrational spectra showed characteristic group frequencies corresponding to a polypeptide structure. No spectral differences were observed by room light effect on the polymer on rutile. However, the polymer obtained in the presence of anatase and room light shows spectral changes associated with the formation of shorter new abundant and conformationally different species compared with the original polymer. The SEM-EDX characterization of the solid phase involved in the thermal synthesis showed that the morphology of the polypeptide is different in the presence of rutile compared to anatase. The SDS-PAGE and GPC results suggest that smaller chains are formed in the presence of both oxides and the distribution of the size and weight of each polymer molecule is completely different when the condensation is performed in the presence of anatase or rutile. Nuclear magnetic resonance analyses confirmed the incorporation of both Gly and Gln residues in the polymers, with a prevalence of Gly. Both possible sequences -GlyGln- and -GlnGly- were also detected.},
keywords = {amino-acids, chemistry, condensation conditions, crystalline diketopiperazine, dioxide, dynamics, earth formation ft-ir glutamic glycine, peptide prebiotic primitive reaction, self-disproportionation, spectra, spectroscopy, synthesis, thermal titanium vibrational},
pubstate = {published},
tppubtype = {article}
}