Sr2+-neutral molecules interactions: An assessment of theoretical procedures

Eizaguirre, Ane; Yáñez, Manuel; Tortajada, Jeanine; Salpin, Jean‐Yves

doi:10.1016/j.cplett.2008.09.006

Cited by 9 publications

(12 citation statements)

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“…The best performing method depends on the metal: when M = Ca the best performing model is BLYP/6-31G(d) while when M = Sr the best one is G96LYP/6-31+G(d,p); it gives almost the same value as the reference. This latter result is in agreement with previous assessments, 79 and this level is the one used in geometry optimization for the Sr containing system. Therefore, we have selected these methods for a subsequent assessment evaluating the whole PES, comparing geometries and relative energies (vide infra).…”

Section: Preliminary Assessmentsupporting

confidence: 92%

A RRKM study and a DFT assessment on gas-phase fragmentation of formamide–M2+ (M = Ca, Sr)

Martín-Sómer

Gaigeot

Yáñez

et al. 2014

Phys. Chem. Chem. Phys.

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A kinetic study of the unimolecular reactivity of formamide-M(2+) (M = Ca, Sr) systems was carried out by means of RRKM statistical theory using high-level DFT. The results predict M(2+), [M(NH2)](+) and [HCO](+) as the main products, together with an intermediate that could eventually evolve to produce [M(NH3)](2+) and CO, for high values of internal energy. In this framework, we also evaluated the influence of the external rotational energy on the reaction rate constants. In order to find a method to perform reliable electronic structure calculations for formamide-M(2+) (M = Ca, Sr) at a relatively low computational cost, an assessment of different methods was performed. In the first assessment twenty-one functionals, belonging to different DFT categories, and an MP2 wave function method using a small basis set were evaluated. CCSD(T)/cc-pWCVTZ single point calculations were used as reference. A second assessment has been performed on geometries and energies. We found BLYP/6-31G(d) and G96LYP/6-31+G(d,p) as the best performing methods, for formamide-Ca(2+) and formamide-Sr(2+), respectively. Furthermore, a detailed assessment was done on RRKM reactivity and G96LYP/6-31G(d) provided results in agreement with higher level calculations. The combination of geometrical, energetics and kinetics (RRKM) criteria to evaluate DFT functionals is rather unusual and provides an original assessment procedure. Overall, we suggest using G96LYP as the best performing functional with a small basis set for both systems.

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Section: Preliminary Assessmentsupporting

confidence: 92%

A RRKM study and a DFT assessment on gas-phase fragmentation of formamide–M2+ (M = Ca, Sr)

Martín-Sómer

Gaigeot

Yáñez

et al. 2014

Phys. Chem. Chem. Phys.

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“…In particular, Schwarz made a significant contribution to the understanding of the alkylation of amines by methylmetal complexes, the metals being Zn, Cd and Hg [7,8]. During these last twenty years our groups also adopted this synergy to study a variety of chemical systems involving the interaction of metal ions with organic molecules and biomolecules [9][10][11][12][13][14][15][16][17]. Notably, we examined in great detail the interactions of uracil and thymine with different metal ions, and compare the unimolecular reactivity observed with copper, [18][19][20] calcium, [21][22][23][24] or heavier metals [25][26][27][28][29].…”

Section: Accepted Manuscript Introductionmentioning

confidence: 99%

Alkylation of uracil and thymine in the gas phase through interaction with alkylmercury compounds

Salpin

Haldys

Latrous

et al. 2019

International Journal of Mass Spectrometry

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“…Also, divalent metal cation is suggested to be involved in DNA binding, DNA‐protein recognition, base flipping, RNA folding, and catalysis 17. The previous experimental and theoretical studies10, 18–34 on simplest building blocks of peptides and proteins were able to model the interaction that occurs between metal ions and large biological molecules. Hoyau et al 22.…”

Section: Introductionmentioning

confidence: 99%

Interaction studies of cysteine with Li⁺, Na⁺, K⁺, Be²⁺, Mg²⁺, and Ca²⁺metal cation complexes

Shankar

Kolandaivel

Senthilkumar

2010

J of Physical Organic Chem

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The coordination geometries, electronic features, metal ion affinities, entropies, and the energetics of Li+, Na+, K+, Be2+, Mg2+, and Ca2+ metal cations with different possible conformations of cysteine complexes were studied. The complexes were optimized using density functional theory (B3LYP) and second order Moller–Plesset Perturbation (MP2) theory methods using 6‐311 + +G** basis set. The interactions of the metal cations at different nucleophilic sites of cysteine conformations were considered after a careful selection among several binding sites. All the metal cations coordinate with cysteine in a tridentate manner and also the most preferred position for the interaction. It is found that, the overall structural parameters of cysteine are not altered by metal ion substitution, but, the metal ion‐binding site has undergone a noticeable change. All the complexes were characterized by an electrostatic interaction between ligand and metal ions that appears slightly more pronounced for lithium and beryllium metal complexes. The metal ion affinity (MIA) and basis set superposition error (BSSE) corrected interaction energy were also computed for all the complexes. The effect of metal cations on the infrared (IR) stretching vibrational modes of amino NH bond, side chain thiol group SH bond, hydroxyl OH bond, and Carbonyl CO bond in cysteine molecules have also been studied. The nature of the metal ion‐ligand bond and the coordination properties were examined using natural bond order (NBO) at bond critical point (electron density and their Laplacian of electron density) through Atoms in Molecules (AIM) analyses. Copyright © 2010 John Wiley & Sons, Ltd.

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Sr2+-neutral molecules interactions: An assessment of theoretical procedures

Cited by 9 publications

References 50 publications

A RRKM study and a DFT assessment on gas-phase fragmentation of formamide–M2+ (M = Ca, Sr)

A RRKM study and a DFT assessment on gas-phase fragmentation of formamide–M2+ (M = Ca, Sr)

Alkylation of uracil and thymine in the gas phase through interaction with alkylmercury compounds

Interaction studies of cysteine with Li⁺, Na⁺, K⁺, Be²⁺, Mg²⁺, and Ca²⁺metal cation complexes

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Sr2+-neutral molecules interactions: An assessment of theoretical procedures

Cited by 9 publications

References 50 publications

A RRKM study and a DFT assessment on gas-phase fragmentation of formamide–M2+ (M = Ca, Sr)

A RRKM study and a DFT assessment on gas-phase fragmentation of formamide–M2+ (M = Ca, Sr)

Alkylation of uracil and thymine in the gas phase through interaction with alkylmercury compounds

Interaction studies of cysteine with Li+, Na+, K+, Be2+, Mg2+, and Ca2+metal cation complexes

Contact Info

Product

Resources

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Interaction studies of cysteine with Li⁺, Na⁺, K⁺, Be²⁺, Mg²⁺, and Ca²⁺metal cation complexes