Coordination Properties of the Oxime Analogue of Glycine to Cu(II)

Georgieva, Ivelina; Trendafilova, Natasha; Rodrı́guez-Santiago, Luis; Sodupe, Mariona

doi:10.1021/jp050626h

Cited by 47 publications

(41 citation statements)

References 46 publications

(92 reference statements)

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“…Consistently, no covalent bonds between Ca and the serine basic centers are found in the NBO analysis, whereas the The partially covalent character of the interactions with Cu is also reflected in the electron density at the corresponding BCPs, which are about twice as large as those calculated for the corresponding Ca 2+ complex. 52 Conversely, the behavior of calcium towards serine is quite similar to that exhibited towards uracil, 53 thiouracils, 53 urea, and thiourea. The significant differences in the reorganization of the electron density of the serine, when interacting with Cu 2+ and Ca 2+ , have their origin in the huge difference between the recombination energy for both dications (20.29 eV for Cu 2+ but only 12.03 eV for Ca 2+ ).…”

Section: Resultsmentioning

confidence: 83%

Serine–Ca²⁺versus serine–Cu²⁺complexes — A theoretical perspective

2010

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The association of Ca 2+ and Cu 2+ to serine was investigated by means of B3LYP DFT calculations. The [serine-M] 2+ (M = Ca, Cu) potential energy surfaces include, as does the neutral serine, a large number of conformers, in which a drastic reorganization of the electron density of the serine moiety is observed. This leads to significant changes in the number and strength of the intramolecular hydrogen bonds existing in the neutral serine tautomers. In some cases, a proton is transferred from the carboxylic OH group to the amino group and accordingly, some of the more stable [serine-M] 2+ complexes can be viewed as the result of the interaction of the zwiterionic form of serine with the doubly charged metal ion. Whereas the interaction between Ca 2+ and serine is essentially electrostatic, that between Cu 2+ and serine has a non-negligible covalent character, reflected in larger electron densities at the bond critical points between the metal and the base, in the negative values of the electron density between the two interacting systems, and in much larger Cu 2+ than Ca 2+ binding energies. More importantly, the interaction with Cu 2+ is followed by a partial oxidation of the base, which is not observed when the metal ion is Ca 2+ . The main consequence is that in Cu 2+ complexes a significant acidity enhancement of the serine moiety takes place, which strongly favors the deprotonation of the [serine-Cu] 2+ complexes. This is not the case for Ca 2+ complexes. Thus, [serine-Ca] 2+ complexes, like those formed by urea, thiourea, selenourea, or glycine, should be detected in the gas phase. Conversely, the complexes with Cu 2+ should deprotonate spontaneously and therefore only [(serine-H)-Cu] + monocations should be experimentally accessible. Résumé :On étudié l'association des cations Ca 2+ et Cu 2+ avec la serine en utilisant la théorie de la fonctionnelle de la densité, B3LYP. Pour l'ion [sérine-M] 2+ (M = Ca, Cu), comme c'est le cas pour la sérine neutre, les surfaces d'énergie potentielle comportent un grand nombre de conformères dans lesquels on peut observer une réorganisation drastique de la densité électronique de la sérine. Ces changements conduisent à des changements significatifs dans le nombre et la force des liaisons hydrogènes intramoléculaires par rapport à celles qui existent dans les tautomères neutres de la sérine. Dans quelques cas, il se produit un transfert de proton du groupe OH de l'acide carboxylique vers le groupe amino et, en conséquence, un certain nombre des complexes les plus stables de l'ion [sérine-M] 2+ peuvent être considérés comme étant le résultat de l'interaction de la forme zwitterionique de la sérine avec l'ion métallique doublement chargé. Alors que l'interaction entre la Ca 2+ et la sérine est essentiellement électrostatique, celle entre le Cu 2+ et la sérine comporte un caractère covalent non négligeable qui est le reflet de densités électroniques plus grandes aux points critiques de liaison entre les deux systèmes en interaction ainsi que des énergies de liaisons beaucoup ...

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Section: Resultsmentioning

confidence: 83%

Serine–Ca²⁺versus serine–Cu²⁺complexes — A theoretical perspective

2010

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“…The application of the B3LYP method to metal ion-water systems has proved a reasonable success. [52][53][54][55] For open-shell Cu 2+ -ligand systems with low coordination numbers (n ) 1, 2) it has been reported [56][57][58] that B3LYP binding energies are overestimated compared to CCSD(T) results. However, the B3LYP relative energies for systems with similar spin density distribution are in good agreement with those determined by highly correlated electronic structure methods.…”

Section: Methodsmentioning

confidence: 99%

Hydration of Copper(II): New Insights from Density Functional Theory and the COSMO Solvation Model

et al. 2008

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The hydrated structure of the Cu(II) ion has been a subject of ongoing debate in the literature. In this article, we use density functional theory (B3LYP) and the COSMO continuum solvent model to characterize the structure and stability of [Cu(H 2 2+ clusters as a function of coordination number (4, 5, and 6) and cluster size (n ) 4-18). We find that the most thermodynamically favored Cu(II) complexes in the gas phase have a very open four-coordinate structure. They are formed from a stable square-planar [Cu(H 2 O) 8 ] 2+ core stabilized by an unpaired electron in the Cu(II) ion d x 2 -y 2 orbital. This is consistent with cluster geometries suggested by recent mass-spectrometric experiments. In the aqueous phase, we find that the more compact five-coordinate square-pyramidal geometry is more stable than either the four-coordinate or six-coordinate clusters in agreement with recent combined EXAFS and XANES studies of aqueous solutions of Cu(II). However, a small energetic difference (∼1.4 kcal/mol) between the five-and six-coordinate models with two full hydration shells around the metal ion suggests that both forms may coexist in solution.

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“…Density functional methods have been shown to be cost-effective methods and have been used to study a wide variety of closed-shell systems with great accuracy (Koch & Holthausen 2001;Sholl & Steckel 2009;Sousa et al 2007). However, for open-shell systems, calculations carried out by some of us have demonstrated that functionals with a larger percentage of exact exchange, such as BHLYP, provide better results compared to the highly correlated CCSD(T) method (Georgieva et al 2005;Poater et al 2004;Rimola et al 2006;Sodupe et al 1999). This is due to the fact that GGA or hybrid functionals with small percentages of exact exchange such as B3LYP overstabilize too delocalized situations, as a result of a bad cancellation of the self-interaction part by the exchange-correlation functional.…”

Section: Computational Detailsmentioning

confidence: 99%

Computational Study of Interstellar Glycine Formation Occurring at Radical Surfaces of Water-Ice Dust Particles

Rimola¹,

Sodupe²,

Ugliengo³

2012

ApJ

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Glycine is the simplest amino acid, and due to the significant astrobiological implications that suppose its detection, the search for it in the interstellar medium (ISM), meteorites, and comets is intensively investigated. In the present work, quantum mechanical calculations based on density functional theory have been used to model the glycine formation on water-ice clusters present in the ISM. The removal of either one H atom or one electron from the water-ice cluster has been considered to simulate the effect of photolytic radiation and of ionizing particles, respectively, which lead to the formation of OH • radical and H 3 O + surface defects. The coupling of incoming CO molecules with the surface OH • radicals on the ice clusters yields the formation of the COOH • radicals via ZPE-corrected energy barriers and reaction energies of about 4-5 kcal mol −1 and −22 kcal mol −1 , respectively. The COOH • radicals couple with incoming NH=CH 2 molecules (experimentally detected in the ISM) to form the NHCH 2 COOH • radical glycine through energy barriers of 12 kcal mol −1 , exceedingly high at ISM cryogenic temperatures. Nonetheless, when H 3 O + is present, one proton may be barrierless transferred to NH=CH 2 to give NH 2 =CH 2 + . This latter may react with the COOH • radical to give the NH 2 CH 2 COOH +• glycine radical cation which can then be transformed into the NH 2 CHC(OH) 2 +• species (the most stable form of glycine in its radical cation state) or into the NH 2 CHCOOH • neutral radical glycine. Estimated rate constants of these events suggest that they are kinetically feasible at temperatures of 100-200 K, which indicate that their occurrence may take place in hot molecular cores or in comets exposed to warmer regions of solar systems. Present results provide quantum chemical evidence that defects formed on water ices due to the harsh-physical conditions of the ISM may trigger reactions of cosmochemical interest. The relevance of surface H 3 O + ions to facilitate chemical processes by proton transfer (i.e., acting as acidic catalysts) is highlighted, and plausible ways of their formation at the water-ice surface in the ISM are also discussed.

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Coordination Properties of the Oxime Analogue of Glycine to Cu(II)

Cited by 47 publications

References 46 publications

Serine–Ca²⁺versus serine–Cu²⁺complexes — A theoretical perspective

Serine–Ca²⁺versus serine–Cu²⁺complexes — A theoretical perspective

Hydration of Copper(II): New Insights from Density Functional Theory and the COSMO Solvation Model

Computational Study of Interstellar Glycine Formation Occurring at Radical Surfaces of Water-Ice Dust Particles

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Coordination Properties of the Oxime Analogue of Glycine to Cu(II)

Cited by 47 publications

References 46 publications

Serine–Ca2+versus serine–Cu2+complexes — A theoretical perspective

Serine–Ca2+versus serine–Cu2+complexes — A theoretical perspective

Hydration of Copper(II): New Insights from Density Functional Theory and the COSMO Solvation Model

Computational Study of Interstellar Glycine Formation Occurring at Radical Surfaces of Water-Ice Dust Particles

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Serine–Ca²⁺versus serine–Cu²⁺complexes — A theoretical perspective

Serine–Ca²⁺versus serine–Cu²⁺complexes — A theoretical perspective