| 1. |
- Bustelo, Emilio, et al.
(author)
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On the Critical Effect of the Metal (Mo vs. W) on the [3+2] Cycloaddition Reaction of M3S4 Clusters with Alkynes : Insights from Experiment and Theory
- 2015
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In: Chemistry - A European Journal. - : Wiley. - 0947-6539 .- 1521-3765. ; 21:42, s. 14823-14833
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Journal article (peer-reviewed)abstract
- Whereas the cluster [Mo3S4(acac)(3)(py)(3)](+) ([1](+), acac=acetylacetonate, py=pyridine) reacts with a variety of alkynes, the cluster [W3S4(acac)(3)(py)(3)](+) ([2](+)) remains unaffected under the same conditions. The reactions of cluster [1]+ show polyphasic kinetics, and in all cases clusters bearing a bridging dithiolene moiety are formed in the first step through the concerted [3+2] cycloaddition between the C equivalent to C atoms of the alkyne and a Mo(mu-S)(2) moiety of the cluster. A computational study has been conducted to analyze the effect of the metal on these concerted [3+ 2] cycloaddition reactions. The calculations suggest that the reactions of cluster [2](+) with alkynes feature Delta G(+) values only slightly larger than its molybdenum analogue, however, the differences in the reaction free energies between both metal clusters and the same alkyne reach up to approximately 10 kcal mol(-1), therefore indicating that the differences in the reactivity are essentially thermodynamic. The activation strain model (ASM) has been used to get more insights into the critical effect of the metal center in these cycloadditions, and the results reveal that the change in reactivity is entirely explained on the basis of the differences in the interaction energies E-int between the cluster and the alkyne. Further decomposition of the E-int values through the localized molecular orbital-energy decomposition analysis (LMO-EDA) indicates that substitution of the Mo atoms in cluster [1](+) by W induces changes in the electronic structure of the cluster that result in weaker intra-and inter-fragment orbital interactions.
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| 2. |
- Pino-Chamorro, Jose Ángel, et al.
(author)
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Mechanism of [3+2] Cycloaddition of Alkynes to the [Mo3S4(acac)(3)(py)(3)][PF6] Cluster
- 2015
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In: Chemistry - A European Journal. - : Wiley-VCH Verlagsgesellschaft. - 0947-6539 .- 1521-3765. ; 21:7, s. 2835-2844
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Journal article (peer-reviewed)abstract
- A study, involving kinetic measurements on the stopped-flow and conventional UV/Vis timescales, ESI-MS, NMR spectroscopy and DFT calculations, has been carried out to understand the mechanism of the reaction of [Mo3S4(acac)(3)(py)(3)][PF6] ([1]PF6; acac = acetylacetonate, py = pyridine) with two RC equivalent to CR alkynes (R = CH2OH (btd), COOH (adc)) in CH3CN. Both reactions show polyphasic kinetics, but experimental and computational data indicate that alkyne activation occurs in a single kinetic step through a concerted mechanism similar to that of organic [3+2] cycloaddition reactions, in this case through the interaction with one Mo(mu-S)(2) moiety of [1](+). The rate of this step is three orders of magnitude faster for adc than that for btd, and the products initially formed evolve in subsequent steps into compounds that result from substitution of py ligands or from reorganization to give species with different structures. Activation strain analysis of the [3+2] cycloaddition step reveals that the deformation of the two reactants has a small contribution to the difference in the computed activation barriers, which is mainly associated with the change in the extent of their interaction at the transition-state structures. Subsequent frontier molecular orbital analysis shows that the carboxylic acid substituents on adc stabilize its HOMO and LUMO orbitals with respect to those on btd due to better electron-withdrawing properties. As a result, the frontier molecular orbitals of the cluster and alkyne become closer in energy; this allows a stronger interaction.
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| 3. |
- Algarra, Andres G.
(author)
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Computational Insights into the Isomerism of Hexacoordinate Metal-Sarcophagine Complexes : The Relationship between Structure and Stability
- 2015
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In: European Journal of Inorganic Chemistry. - : Wiley. - 1434-1948 .- 1099-1948 .- 1099-0682. ; :3, s. 503-511
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Journal article (peer-reviewed)abstract
- The hexacoordinate complexes that the macrobicyclic ligands {(NH3)(2)sar)(2+) and {NMe3)(2)sar}(2+) (sar = 3,6,10,13,16,19-hexaazabicyclo[6.6.6]icosane) form with transition metals such as Co-III, Co-II and Cu-II can adopt several isomeric structures. In this article, we have firstly employed DFT methods lo compute the relative stability of their Delta-ob(3), Delta-ob(2)lel, Delta-lel(2)ob and Delta-lel(3) isomers, as well as the activation barriers for their interconversion. In agreement with the experimental data, the results show that, in general, the different isomers of the Co-III and Co-II complexes present similar free energies, whereas the Cu-II complexes show a strong tendency towards the lel(3) form. In addition, the interplay between the structure and stability of these species has been studied by combining shape maps with a distortion/interaction energy analysis. In contrast to the geometries close to the ideal octahedron that all the studied Co complexes present, the le)3 structures of [Cu{(NH3)(2)sar}](4+) and [Cu{(NMe3)(2)sar](4+) are better described. as trigonal prisms. In such structures the ligand adopts a conformation significantly more stable than in the other isomers, and this drives the formation of lel(3)-[Cu{(NH3)(2)sar}](4+) and lel(3)-[Cu{(NNe3)(2)sar}](4+). Overall, the results show a clear relationship between the stability of a given isomer and its degree of distortion with respect to the ideal octahedron (or trigonal prism), with the latter being ultimately dependent on the transition metal and its radius.
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| 4. |
- Algarra, Andres G., et al.
(author)
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Computational Insights on the Geometrical Arrangements of Cu(II) with a Mixed-Donor N3S3 Macrobicyclic Ligand
- 2014
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In: Inorganic Chemistry. - : American Chemical Society (ACS). - 0020-1669 .- 1520-510X. ; 53:1, s. 512-521
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Journal article (peer-reviewed)abstract
- The macrobicyclic mixed-donor N3S3 cage ligand AMME-N(3)S(3)sar (1-methyl-8-amino-3,13,16-trithia-6,10,19-triazabicyclo[6.6.6]eicosane) can form complexes with Cu(II) in which it acts as hexadentate (N3S3) or tetradentate (N2S2) donor. These two complexes are in equilibrium that is strongly influenced by the presence of halide ions (Br- and Cl-) and the nature of the solvent (DMSO, MeCN, and H2O). In the absence of halides the hexadentate coordination mode of the ligand is preferred and the encapsulated complex (Cu-in(2+)) is formed. Addition of halide ions in organic solvents (DMSO or MeCN) leads to the tetradentate complex (Cu-out(+)) in a polyphasic kinetic process, but no Cu-out(+) complex is formed when the reaction is performed in water. Here we applied density functional theory calculations to study the mechanism of this interconversion as well as to understand the changes in the reactivity associated with the presence of water. Calculations were performed at the B3LYP/(SDD,6-31G**) level, in combination with continuum (MeCN) or discrete-continuum (H2O) solvent models. Our results show that formation of Cu-out(+) in organic media is exergonic and involves sequential halide-catalyzed inversion of the configuration of a N-donor of the macrocycle, rapid halide coordination, and inversion of the configuration of a S-donor. In aqueous solution the solvent is found to have an effect on both the thermodynamics and the kinetics of the reaction. Thermodynamically, the process becomes endergonic mainly due to the preferential solvation of halide ions by water, while the kinetics is influenced by formation of a network of H-bonded water molecules that surrounds the complex.
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| 5. |
- Daver, Henrik, et al.
(author)
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Mixed Explicit-Implicit Solvation Approach for Modeling of Alkane Complexation in Water-Soluble Self-Assembled Capsules
- 2018
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In: Journal of the American Chemical Society. - : American Chemical Society (ACS). - 0002-7863 .- 1520-5126. ; 140:39, s. 12527-12537
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Journal article (peer-reviewed)abstract
- The host-guest binding properties of a water-soluble resorcinarene-based cavitand are examined using density functional theory methodology. Experimentally, the cavitand has been observed to self-assemble in aqueous solution into both 1:1 and 2:1 host/guest complexes with hydrophobic guests such as n-alkanes. For n-decane, equilibrium was observed between the 1:1 and 2:1 complexes, while 1:1 complexes are formed with shorter n-alkanes and 2:1 complexes are formed with longer ones. These findings are used to assess the standard quantum chemical methodology. It is first shown that a rather advanced com- putational protocol (B3LYP-D3(BJ)/6-311+G(2d,2p) with COSMO-RS and quasi-rigid-rotor-harmonic-oscillator) gives very large errors. Systematic examination of the various elements of the methodology shows that the error stems from the implicit solvation model. A mixed explicit-implicit solvation protocol is developed that involves a parametrization of the hydration free energy of water such that water cluster formation in water is predicted to be thermoneutral. This new approach is demonstrated to lead to a major improvement in the calculated binding free energies of n-alkanes, reproducing very well the 1:1 versus 2:1 host/guest binding trends.
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| 6. |
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| 7. |
- Lundberg, Helena, et al.
(author)
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Mechanistic Elucidation of Zirconium-Catalyzed Direct Amidation
- 2017
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In: Journal of the American Chemical Society. - : American Chemical Society (ACS). - 0002-7863 .- 1520-5126. ; 139:6, s. 2286-2295
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Journal article (peer-reviewed)abstract
- The mechanism of the zirconium-catalyzed condensation of carboxylic acids and amines for direct formation of amides was studied using kinetics, NMR spectroscopy, and DFT calculations. The reaction is found to be first order with respect to the catalyst and has a positive rate dependence on amine concentration. A negative rate dependence on carboxylic acid concentration is observed along with S-shaped kinetic profiles under certain conditions, which is consistent with the formation of reversible off-cycle species. Kinetic experiments using reaction progress kinetic analysis protocols demonstrate that inhibition of the catalyst by the amide product can be avoided using a high amine concentration. These insights led to the design of a reaction protocol with improved yields and a decrease in catalyst loading. NMR spectroscopy provides important details of the nature of the zirconium catalyst and serves as the starting point for a theoretical study of the catalytic cycle using DFT calculations. These studies indicate that a dinuclear zirconium species can catalyze the reaction with feasible energy barriers. The amine is proposed to perform a nucleophilic attack at a terminal eta(2)-carboxylate ligand of the zirconium catalyst, followed by a C-O bond cleavage step, with an intermediate proton transfer from nitrogen to oxygen facilitated by an additional equivalent of amine. In addition, the DFT calculations reproduce experimentally observed effects on reaction rate, induced by electronically different substituents on the carboxylic acid.
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