2017 |
Mendizabal, F; Mera-Adasme, R; Xu, W H; Sundholm, D Electronic and Optical Properties of Metalloporphyrins of Zinc on Tio2 Cluster in Dye-Sensitized Solar-Cells (Dssc). A Quantum Chemistry Study Artículo de revista Rsc Advances, 7 (68), pp. 42677-42684, 2017. Resumen | Enlaces | BibTeX | Etiquetas: approximation, efficient, energy-levels, excited-states, performance, porphyrin pseudopotentials, sensitizers, surface, thermochemistry @article{mendizabal2017electronic, title = {Electronic and Optical Properties of Metalloporphyrins of Zinc on Tio2 Cluster in Dye-Sensitized Solar-Cells (Dssc). A Quantum Chemistry Study}, author = { F. Mendizabal and R. Mera-Adasme and W.H. Xu and D. Sundholm}, url = {/brokenurl#<Go to ISI>://WOS:000409548200006}, doi = {10.1039/c7ra08648b}, year = {2017}, date = {2017-01-01}, journal = {Rsc Advances}, volume = {7}, number = {68}, pages = {42677-42684}, abstract = {Dye-sensitized solar-cell (DSSC) systems have been investigated by calculating light-absorption and electron-injection processes of the LD13 ([5,15-bis(2,6-(1,1-dimethylethyl)-phenyl)-10-4-dimethylaminophenylethynyl-20-4-carboxy phenylethynyl porphyrinato]zinc-(II)) and YD2-o-C8 ([5,15bis( 2,6-dioctoxyphenyl)-10-(bis(4-hexylphenyl)amino-20-4-carboxyphenylethynyl)porphyrinato]zinc-(II)) dyes adsorbed on a TiO2 cluster simulating the semiconductor. The binding energy of the dyes with the TiO2 clusters has been calculated at the density functional theory (DFT) level using the B3LYP and CAM-B3LYP functionals. The electronic excitation energies have been calculated at the time-dependent DFT (TDDFT) level for the dyes in the gas and solvent phase employing the B3LYP, CAM-B3LYP and BHLYP functionals. The calculated excitation energies have been compared to values obtained at the algebraic diagrammatic construction through second order (ADC(2)) level of theory. The TDDFT calculations with the B3LYP in tetrahydrofuran solvent with the dye and dye-TiO2 models yield excitation energies that agree well with the transitions in the experimental absorption spectra. Changes in the free energy for electron injection support the better performance of the dyes on the TiO2 clusters.}, keywords = {approximation, efficient, energy-levels, excited-states, performance, porphyrin pseudopotentials, sensitizers, surface, thermochemistry}, pubstate = {published}, tppubtype = {article} } Dye-sensitized solar-cell (DSSC) systems have been investigated by calculating light-absorption and electron-injection processes of the LD13 ([5,15-bis(2,6-(1,1-dimethylethyl)-phenyl)-10-4-dimethylaminophenylethynyl-20-4-carboxy phenylethynyl porphyrinato]zinc-(II)) and YD2-o-C8 ([5,15bis( 2,6-dioctoxyphenyl)-10-(bis(4-hexylphenyl)amino-20-4-carboxyphenylethynyl)porphyrinato]zinc-(II)) dyes adsorbed on a TiO2 cluster simulating the semiconductor. The binding energy of the dyes with the TiO2 clusters has been calculated at the density functional theory (DFT) level using the B3LYP and CAM-B3LYP functionals. The electronic excitation energies have been calculated at the time-dependent DFT (TDDFT) level for the dyes in the gas and solvent phase employing the B3LYP, CAM-B3LYP and BHLYP functionals. The calculated excitation energies have been compared to values obtained at the algebraic diagrammatic construction through second order (ADC(2)) level of theory. The TDDFT calculations with the B3LYP in tetrahydrofuran solvent with the dye and dye-TiO2 models yield excitation energies that agree well with the transitions in the experimental absorption spectra. Changes in the free energy for electron injection support the better performance of the dyes on the TiO2 clusters. |
2016 |
Inostroza, N; Mendizabal, F; Arratia-Pérez, R; Orellana, C; Linares-Flores, C Improvement of Photovoltaic Performance by Substituent Effect of Donor and Acceptor Structure of Tpa-Based Dye-Sensitized Solar Cells Artículo de revista Journal of Molecular Modeling, 22 (1), 2016, ISSN: 1610-2940. Resumen | Enlaces | BibTeX | Etiquetas: approximation, cells, density design, dye-sensitized electron-transfer, electronic energy-levels, free functional molecular organic organic-dyes, porphyrins, semiconductor, solar spectra, surface theory, tio2 @article{RN307, title = {Improvement of Photovoltaic Performance by Substituent Effect of Donor and Acceptor Structure of Tpa-Based Dye-Sensitized Solar Cells}, author = { N. Inostroza and F. Mendizabal and R. Arratia-P\'{e}rez and C. Orellana and C. Linares-Flores}, url = {/brokenurl#<Go to ISI>://WOS:000369312100025}, doi = {10.1007/s00894-015-2893-9}, issn = {1610-2940}, year = {2016}, date = {2016-01-01}, journal = {Journal of Molecular Modeling}, volume = {22}, number = {1}, abstract = {We report a computational study of a series of organic dyes built with triphenylamine (TPA) as an electron donor group. We designed a set of six dyes called (TPA-n, where n=0-5). In order to enhance the electron-injection process, the electron-donor effect of some specific substituent was studied. Thus, we gave insights into the rational design of organic TPA-based chromophores for use in dye-sensitized solar cells (DSSCs). In addition, we report the HOMO, LUMO, the calculated excited state oxidized potential E-dye*(eV) and the free energy change for electron-injection Delta G(inject)(eV), and the UV-visible absorption bands for TPA-n dyes by a time-dependent density functional theory (TDDFT) procedure at the B3LYP and CAM-B3LYP levels with solvent effect. The results demonstrate that the introduction of the electron-acceptor groups produces an intramolecular charge transfer showing a shift of the absorption wavelengths of TPA-n under studies.}, keywords = {approximation, cells, density design, dye-sensitized electron-transfer, electronic energy-levels, free functional molecular organic organic-dyes, porphyrins, semiconductor, solar spectra, surface theory, tio2}, pubstate = {published}, tppubtype = {article} } We report a computational study of a series of organic dyes built with triphenylamine (TPA) as an electron donor group. We designed a set of six dyes called (TPA-n, where n=0-5). In order to enhance the electron-injection process, the electron-donor effect of some specific substituent was studied. Thus, we gave insights into the rational design of organic TPA-based chromophores for use in dye-sensitized solar cells (DSSCs). In addition, we report the HOMO, LUMO, the calculated excited state oxidized potential E-dye*(eV) and the free energy change for electron-injection Delta G(inject)(eV), and the UV-visible absorption bands for TPA-n dyes by a time-dependent density functional theory (TDDFT) procedure at the B3LYP and CAM-B3LYP levels with solvent effect. The results demonstrate that the introduction of the electron-acceptor groups produces an intramolecular charge transfer showing a shift of the absorption wavelengths of TPA-n under studies. |
Munoz-Castro, A; Gomez, T; Carey, D M; Miranda-Rojas, S; Mendizabal, F; Zagal, J H; Arratia-Perez, R Surface on Surface. Survey of the Monolayer Gold-Graphene Interaction from Au-12 and Pah Via Relativistic Dft Calculations Artículo de revista Journal of Physical Chemistry C, 120 (13), pp. 7358-7364, 2016, ISSN: 1932-7447. Resumen | Enlaces | BibTeX | Etiquetas: ab-initio, approximation, chemistry clusters, density-functional generalized gradient hydrogen-bonds, interaction, monolayers, noncovalent phthalocyanines, pseudopotentials, self-assembled theory @article{RN303, title = {Surface on Surface. Survey of the Monolayer Gold-Graphene Interaction from Au-12 and Pah Via Relativistic Dft Calculations}, author = { A. Munoz-Castro and T. Gomez and D.M. Carey and S. Miranda-Rojas and F. Mendizabal and J.H. Zagal and R. Arratia-Perez}, url = {/brokenurl#<Go to ISI>://WOS:000373862700049}, doi = {10.1021/acs.jpcc.5b12580}, issn = {1932-7447}, year = {2016}, date = {2016-01-01}, journal = {Journal of Physical Chemistry C}, volume = {120}, number = {13}, pages = {7358-7364}, abstract = {Gold-graphene interaction at the interface is evaluated through different polyaromatic hydrocarbons (PAH), accounted by C6H6, C24H12, C54H16, and C96H18, focusing into different energetic terms related to the overall interaction. Our results characterize the neutral gold-PAH interaction nature with 45% of dispersion character, 35% of electrostatic, and 20% of covalent character, suggesting that moderate van der Waals character is mostly involved in the interaction, which increases according to the size of the respective PAH. The resulting surface charge distribution in the graphene model is a relevant parameter to take into account, since the ability of the surface charge to be reorganized over the polycyclic structure in both contact and surrounding regions is important in order to evaluate interactions and different interacting conformations. Our results suggest that for a Au-12 contact surface of radius 4.13 angstrom, the covalent, electrostatic and dispersion character of the interaction are effectively accounted in a graphene surface of about 6.18 angstrom, as given by circumcoronene, depicting a critical size where the overall interaction character can be accounted.}, keywords = {ab-initio, approximation, chemistry clusters, density-functional generalized gradient hydrogen-bonds, interaction, monolayers, noncovalent phthalocyanines, pseudopotentials, self-assembled theory}, pubstate = {published}, tppubtype = {article} } Gold-graphene interaction at the interface is evaluated through different polyaromatic hydrocarbons (PAH), accounted by C6H6, C24H12, C54H16, and C96H18, focusing into different energetic terms related to the overall interaction. Our results characterize the neutral gold-PAH interaction nature with 45% of dispersion character, 35% of electrostatic, and 20% of covalent character, suggesting that moderate van der Waals character is mostly involved in the interaction, which increases according to the size of the respective PAH. The resulting surface charge distribution in the graphene model is a relevant parameter to take into account, since the ability of the surface charge to be reorganized over the polycyclic structure in both contact and surrounding regions is important in order to evaluate interactions and different interacting conformations. Our results suggest that for a Au-12 contact surface of radius 4.13 angstrom, the covalent, electrostatic and dispersion character of the interaction are effectively accounted in a graphene surface of about 6.18 angstrom, as given by circumcoronene, depicting a critical size where the overall interaction character can be accounted. |
Mera-Adasme, R; Xu, W H; Sundholm, D; Mendizabal, F Calculations of the Light Absorption Spectra of Porphyrinoid Chromophores for Dye-Sensitized Solar Cells Artículo de revista Physical Chemistry Chemical Physics, 18 (40), pp. 27877-27884, 2016, ISSN: 1463-9076. Resumen | Enlaces | BibTeX | Etiquetas: adsorption, approximation, basis-sets, correlation-energy, dft, efficiency hartree-fock, model, organic-dyes, performance, screening @article{RN305, title = {Calculations of the Light Absorption Spectra of Porphyrinoid Chromophores for Dye-Sensitized Solar Cells}, author = { R. Mera-Adasme and W.H. Xu and D. Sundholm and F. Mendizabal}, url = {/brokenurl#<Go to ISI>://WOS:000385180600020}, doi = {10.1039/c6cp04627d}, issn = {1463-9076}, year = {2016}, date = {2016-01-01}, journal = {Physical Chemistry Chemical Physics}, volume = {18}, number = {40}, pages = {27877-27884}, abstract = {Solar power is a strong alternative to the currently used fossil fuels in order to satisfy the world's energy needs. Among them, dye-sensitized solar cells (DSSC) represent a low-cost option. Efficient and cheap dyes are currently needed to make DSSCs competitive. Computational chemistry can be used to guide the design of new light-absorbing chromophores. Here, we have computationally studied the lowest excited states of ZnPBAT, which is a recently synthesized porphyrinoid chromophore with high light-absorption efficiency. The calculations have been performed at ab initio correlated levels of theory employing second-order coupled clusters (CC2) and algebraic diagrammatic construction using second order (ADC(2)) methods and by performing density functional theory (DFT) calculations using the time-dependent DFT (TDDFT) approach for excitation energies. The ultraviolet-visible (UV-vis) spectrum calculated at the ADC(2) and CC2 levels agrees well with the experimental one. The calculations show that ZnPBAT has six electronic transitions in the visible range of the absorption spectrum. The ab initio correlated calculations and previously reported experimental data have been used to assess the performance of several well-known density functionals that have been employed in the present TDDFT study. Solvent effects have been estimated by using the conductor-like screening model (COSMO). The influence of the addition of a TiO2 cluster to the chromophore systems has also been investigated. The results indicate that both CAM-B3LYP and Becke's "half-and-half'' (BHLYP) density functionals are appropriate for the studies of excitation energies in the blue range of the visible spectrum for these kinds of porphyrinoid chromophores, whereas the excitation energies of the Q band calculated at the ab initio correlated level are more accurate than those obtained in the present TDDFT calculations. The inclusion of solvent effects has a modest influence on the spectrum of the protonated form of the studied chromophores, whereas solvent models are crucial when studying the absorption spectrum of the anionic chromophore. The calculated UV-vis spectrum for the chromophore anion is not significantly affected by attaching a TiO2 cluster to it.}, keywords = {adsorption, approximation, basis-sets, correlation-energy, dft, efficiency hartree-fock, model, organic-dyes, performance, screening}, pubstate = {published}, tppubtype = {article} } Solar power is a strong alternative to the currently used fossil fuels in order to satisfy the world's energy needs. Among them, dye-sensitized solar cells (DSSC) represent a low-cost option. Efficient and cheap dyes are currently needed to make DSSCs competitive. Computational chemistry can be used to guide the design of new light-absorbing chromophores. Here, we have computationally studied the lowest excited states of ZnPBAT, which is a recently synthesized porphyrinoid chromophore with high light-absorption efficiency. The calculations have been performed at ab initio correlated levels of theory employing second-order coupled clusters (CC2) and algebraic diagrammatic construction using second order (ADC(2)) methods and by performing density functional theory (DFT) calculations using the time-dependent DFT (TDDFT) approach for excitation energies. The ultraviolet-visible (UV-vis) spectrum calculated at the ADC(2) and CC2 levels agrees well with the experimental one. The calculations show that ZnPBAT has six electronic transitions in the visible range of the absorption spectrum. The ab initio correlated calculations and previously reported experimental data have been used to assess the performance of several well-known density functionals that have been employed in the present TDDFT study. Solvent effects have been estimated by using the conductor-like screening model (COSMO). The influence of the addition of a TiO2 cluster to the chromophore systems has also been investigated. The results indicate that both CAM-B3LYP and Becke's "half-and-half'' (BHLYP) density functionals are appropriate for the studies of excitation energies in the blue range of the visible spectrum for these kinds of porphyrinoid chromophores, whereas the excitation energies of the Q band calculated at the ab initio correlated level are more accurate than those obtained in the present TDDFT calculations. The inclusion of solvent effects has a modest influence on the spectrum of the protonated form of the studied chromophores, whereas solvent models are crucial when studying the absorption spectrum of the anionic chromophore. The calculated UV-vis spectrum for the chromophore anion is not significantly affected by attaching a TiO2 cluster to it. |
2015 |
Linares-Flores, C; Mendizabal, F; Arratia-Perez, R; Inostroza, N; Orellana, C Substituents Role in Zinc Phthalocyanine Derivatives Used as Dye-Sensitized Solar Cells. A Theoretical Study Using Density Functional Theory Artículo de revista Chemical Physics Letters, 639 , pp. 172-177, 2015, ISSN: 0009-2614. Resumen | Enlaces | BibTeX | Etiquetas: approximation, conversion, electronic-structure, hammett organic-dyes, parameters, porphyrins properties, spectroscopic states, surface, tio2 @article{RN251, title = {Substituents Role in Zinc Phthalocyanine Derivatives Used as Dye-Sensitized Solar Cells. A Theoretical Study Using Density Functional Theory}, author = { C. Linares-Flores and F. Mendizabal and R. Arratia-Perez and N. Inostroza and C. Orellana}, url = {/brokenurl#<Go to ISI>://WOS:000365814400033}, doi = {10.1016/j.cplett.2015.09.025}, issn = {0009-2614}, year = {2015}, date = {2015-01-01}, journal = {Chemical Physics Letters}, volume = {639}, pages = {172-177}, publisher = {2015 Elsevier B.V.}, abstract = {A series of zinc phthalocyanine dyes with different electron-donating and electron-withdrawing substituents and using the COOH as the anchor group that interacts with the semiconductor (TiO2) surface, were studied employing DFT and TDDFT methodologies. Their HOMO and LUMO orbital energies and, the redox mediator position would facilitate the injection process toward the conduction band of TiO2. We tested the effect of some electron-donating or electron-withdrawing substituents over zinc phthalocyanine dyes in terms of the Hammett parameters (Sigma sigma). We obtained a linear correlation between the substituents properties versus the free energy change of the electron-injection (Delta G(inject)) process.}, keywords = {approximation, conversion, electronic-structure, hammett organic-dyes, parameters, porphyrins properties, spectroscopic states, surface, tio2}, pubstate = {published}, tppubtype = {article} } A series of zinc phthalocyanine dyes with different electron-donating and electron-withdrawing substituents and using the COOH as the anchor group that interacts with the semiconductor (TiO2) surface, were studied employing DFT and TDDFT methodologies. Their HOMO and LUMO orbital energies and, the redox mediator position would facilitate the injection process toward the conduction band of TiO2. We tested the effect of some electron-donating or electron-withdrawing substituents over zinc phthalocyanine dyes in terms of the Hammett parameters (Sigma sigma). We obtained a linear correlation between the substituents properties versus the free energy change of the electron-injection (Delta G(inject)) process. |
2013 |
Mendizabal, F; Salazar, R Theoretical Study on Electronic Spectra and Interaction in [Au-3]-L-[Au-3] (L = C6f6,Ag+) Complexes Artículo de revista Journal of Molecular Modeling, 19 (5), pp. 1973-1979, 2013, ISSN: 1610-2940. Resumen | Enlaces | BibTeX | Etiquetas: approximation, attraction, chemistry, dimers electronic energies, interaction, mercury, photophysics, secondary spectra @article{RN82, title = {Theoretical Study on Electronic Spectra and Interaction in [Au-3]-L-[Au-3] (L = C6f6,Ag+) Complexes}, author = { F. Mendizabal and R. Salazar}, url = {/brokenurl#<Go to ISI>://WOS:000318274700006}, doi = {10.1007/s00894-012-1570-5}, issn = {1610-2940}, year = {2013}, date = {2013-01-01}, journal = {Journal of Molecular Modeling}, volume = {19}, number = {5}, pages = {1973-1979}, abstract = {The electronic structure and spectroscopic properties of [Au-3(mu-C(OEt) = NC6H4CH3)(3)](n)-(C6F6)(m) and [Au-3(mu-C-2,N-3-bzim)(3)](n)-(Ag+)(m) were studied at the B3LYP, PBE and TPSS levels. The interaction between the [Au-3] cluster and L (C6F6, Ag+) was analyzed. Grimme's dispersion correction is used for those functionals. Weak pi-interactions (Au-C6F6) were found to be the main contribution short-range stability in the models; while in the models with Ag+, an ionic interaction is obtained. The absorption spectra of these models at the PBE level agree with the experimental spectra.}, keywords = {approximation, attraction, chemistry, dimers electronic energies, interaction, mercury, photophysics, secondary spectra}, pubstate = {published}, tppubtype = {article} } The electronic structure and spectroscopic properties of [Au-3(mu-C(OEt) = NC6H4CH3)(3)](n)-(C6F6)(m) and [Au-3(mu-C-2,N-3-bzim)(3)](n)-(Ag+)(m) were studied at the B3LYP, PBE and TPSS levels. The interaction between the [Au-3] cluster and L (C6F6, Ag+) was analyzed. Grimme's dispersion correction is used for those functionals. Weak pi-interactions (Au-C6F6) were found to be the main contribution short-range stability in the models; while in the models with Ag+, an ionic interaction is obtained. The absorption spectra of these models at the PBE level agree with the experimental spectra. |
Mendizabal, F; Donoso, D; Salazar, R 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)) Artículo de revista Journal of the Chilean Chemical Society, 58 (1), pp. 1562-1570, 2013, ISSN: 0717-9707. Resumen | Enlaces | BibTeX | Etiquetas: approximation, chemical-reactivity, chemistry cluster clusters, complexes, crystal-structure, electronegativity, electrophilicity index, interactions, metallic platinum pseudopotentials, reactivity, units @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} } 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. |
2012 |
Burgos, D; Olea-Azar, C; Mendizabal, F Theoretical Study of the Local Reactivity of Electrophiles of the Type Mpr (3) (+) (M = Cu, Ag, Au ;R = -H, -Me, -Ph) Artículo de revista Journal of Molecular Modeling, 18 (5), pp. 2021-2029, 2012, ISSN: 1610-2940. Resumen | Enlaces | BibTeX | Etiquetas: approximation, chemistry complexes, effects, electrophile fragments, gold, hardness, quasi-relativistic reactivity, stability @article{RN86, title = {Theoretical Study of the Local Reactivity of Electrophiles of the Type Mpr (3) (+) (M = Cu, Ag, Au ;R = -H, -Me, -Ph)}, author = { D. Burgos and C. Olea-Azar and F. Mendizabal}, url = {/brokenurl#<Go to ISI>://WOS:000303541900031}, doi = {10.1007/s00894-011-1213-2}, issn = {1610-2940}, year = {2012}, date = {2012-01-01}, journal = {Journal of Molecular Modeling}, volume = {18}, number = {5}, pages = {2021-2029}, abstract = {Reactivity prediction in the series of MPR (3) (+) fragments ( M = Au, Ag, Cu; R = -H, -Me, -Ph) has been achieved at the ab initio (HF and MP2) and density functional theory (B3LYP and PBE) levels. We have used global and local descriptors based on conceptual DFT such as hardness, Fukui function and electrophilicity index. For all methods and fragments, we have found an equal trend in reactivity using both the global and local electrophilicity index: QR-AuPR (3) (+) > CuPR (3) (+) a parts per thousand aEuro parts per thousand AgPR (3) (+) > NR-AuPR (3) (+) . It is also found that the electrophilicity power decreases as the volume of R increases.}, keywords = {approximation, chemistry complexes, effects, electrophile fragments, gold, hardness, quasi-relativistic reactivity, stability}, pubstate = {published}, tppubtype = {article} } Reactivity prediction in the series of MPR (3) (+) fragments ( M = Au, Ag, Cu; R = -H, -Me, -Ph) has been achieved at the ab initio (HF and MP2) and density functional theory (B3LYP and PBE) levels. We have used global and local descriptors based on conceptual DFT such as hardness, Fukui function and electrophilicity index. For all methods and fragments, we have found an equal trend in reactivity using both the global and local electrophilicity index: QR-AuPR (3) (+) > CuPR (3) (+) a parts per thousand aEuro parts per thousand AgPR (3) (+) > NR-AuPR (3) (+) . It is also found that the electrophilicity power decreases as the volume of R increases. |
Mera-Adasme, R; Mendizabal, F; González, M; Miranda-Rojas, S; Olea-Azar, C; Sundholm, D Computational Studies of the Metal-Binding Site of the Wild-Type and the H46r Mutant of the Copper, Zinc Superoxide Dismutase Artículo de revista Inorganic Chemistry, 51 (10), pp. 5561-5568, 2012, ISSN: 0020-1669. Resumen | Enlaces | BibTeX | Etiquetas: amyotrophic-lateral-sclerosis, approximation, correlation-energy, crystal-structures, cu, density efficient, functionals, sod1, solvents zn @article{RN85, title = {Computational Studies of the Metal-Binding Site of the Wild-Type and the H46r Mutant of the Copper, Zinc Superoxide Dismutase}, author = { R. Mera-Adasme and F. Mendizabal and M. Gonz\'{a}lez and S. Miranda-Rojas and C. Olea-Azar and D. Sundholm}, url = {/brokenurl#<Go to ISI>://WOS:000304215200011}, doi = {10.1021/ic202416d}, issn = {0020-1669}, year = {2012}, date = {2012-01-01}, journal = {Inorganic Chemistry}, volume = {51}, number = {10}, pages = {5561-5568}, abstract = {Impairment of the Zn(II)-binding site of the copper, zinc superoxide dismutase (CuZnSOD) protein is involved in a number of hypotheses and explanations for the still unknown toxic gain of function mutant varieties of CuZnSOD that are associated with familial forms of amyotrophic lateral sclerosis (ALS). In this work, computational chemistry methods have been used for studying models of the metal-binding site of the ALS-linked H46R mutant of CuZnSOD and of the wild-type variety of the enzyme. By comparing the energy and electronic structure of these models, a plausible explanation for the effect of the H46R mutation on the zinc site is obtained. The computational study clarifies the role of the D124 and D125 residues for keeping the structural integrity of the Zn(II)-binding site, which was known to exist but its mechanism has not been explained. Earlier results suggest that the explanation for the impairment of the Zn(II)-site proposed in this work may be useful for understanding the mechanism of action of the ALS-linked mutations in CuZnSOD in general.}, keywords = {amyotrophic-lateral-sclerosis, approximation, correlation-energy, crystal-structures, cu, density efficient, functionals, sod1, solvents zn}, pubstate = {published}, tppubtype = {article} } Impairment of the Zn(II)-binding site of the copper, zinc superoxide dismutase (CuZnSOD) protein is involved in a number of hypotheses and explanations for the still unknown toxic gain of function mutant varieties of CuZnSOD that are associated with familial forms of amyotrophic lateral sclerosis (ALS). In this work, computational chemistry methods have been used for studying models of the metal-binding site of the ALS-linked H46R mutant of CuZnSOD and of the wild-type variety of the enzyme. By comparing the energy and electronic structure of these models, a plausible explanation for the effect of the H46R mutation on the zinc site is obtained. The computational study clarifies the role of the D124 and D125 residues for keeping the structural integrity of the Zn(II)-binding site, which was known to exist but its mechanism has not been explained. Earlier results suggest that the explanation for the impairment of the Zn(II)-site proposed in this work may be useful for understanding the mechanism of action of the ALS-linked mutations in CuZnSOD in general. |
2011 |
Mendizabal, F; Donoso, D; Burgos, D Theoretical Study of the Protonation of [Pt-3(Mu-L)(3)(L ')(3)] (L = Co, So2, Cnh; L ' = Ph3, Cnh) Artículo de revista Chemical Physics Letters, 514 (4-6), pp. 374-378, 2011, ISSN: 0009-2614. Resumen | Enlaces | BibTeX | Etiquetas: approximation, chemistry, cluster complexes, electrophilicity hydride, index, molecules, systems, units @article{mendizabal2011theoretical, title = {Theoretical Study of the Protonation of [Pt-3(Mu-L)(3)(L ')(3)] (L = Co, So2, Cnh; L ' = Ph3, Cnh)}, author = { F. Mendizabal and D. Donoso and D. Burgos}, url = {/brokenurl#<Go to ISI>://WOS:000295831700035}, doi = {10.1016/j.cplett.2011.08.068}, issn = {0009-2614}, year = {2011}, date = {2011-01-01}, journal = {Chemical Physics Letters}, volume = {514}, number = {4-6}, pages = {374-378}, publisher = {2011 Elsevier B. V.}, abstract = {Ab initio calculations suggest that a series of clusters of the [Pt-3(mu-L)(3)(L')(3)(mu(3)-H](+) type (L = CO, SO2, CNH; L' = PH3, CNH) are stable. We have studied these clusters at the HF, MP2, B3LYP, PBE and TPSS theory levels. The magnitude of the interaction energies and distances indicates a substantial covalent character of the Pt-3-H bond, confirmed by orbital diagrams. In addition, the Fukui index of electrophilic attack and electrophilicity index on the unprotonated clusters were used to explore possible sites where chemical reactivity may play a role.}, keywords = {approximation, chemistry, cluster complexes, electrophilicity hydride, index, molecules, systems, units}, pubstate = {published}, tppubtype = {article} } Ab initio calculations suggest that a series of clusters of the [Pt-3(mu-L)(3)(L')(3)(mu(3)-H](+) type (L = CO, SO2, CNH; L' = PH3, CNH) are stable. We have studied these clusters at the HF, MP2, B3LYP, PBE and TPSS theory levels. The magnitude of the interaction energies and distances indicates a substantial covalent character of the Pt-3-H bond, confirmed by orbital diagrams. In addition, the Fukui index of electrophilic attack and electrophilicity index on the unprotonated clusters were used to explore possible sites where chemical reactivity may play a role. |